Starting phenix.real_space_refine on Thu Jun 19 21:56:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xmp_38485/06_2025/8xmp_38485_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xmp_38485/06_2025/8xmp_38485.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.11 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xmp_38485/06_2025/8xmp_38485.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xmp_38485/06_2025/8xmp_38485.map" model { file = "/net/cci-nas-00/data/ceres_data/8xmp_38485/06_2025/8xmp_38485_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xmp_38485/06_2025/8xmp_38485_neut.cif" } resolution = 3.11 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.040 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 23 9.91 5 Fe 2 7.16 5 S 218 5.16 5 C 14198 2.51 5 N 4085 2.21 5 O 4423 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 22949 Number of models: 1 Model: "" Number of chains: 15 Chain: "2" Number of atoms: 2263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2263 Classifications: {'peptide': 288} Link IDs: {'PTRANS': 13, 'TRANS': 274} Chain breaks: 2 Chain: "E" Number of atoms: 5455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 718, 5455 Classifications: {'peptide': 718} Link IDs: {'PTRANS': 22, 'TRANS': 695} Chain breaks: 5 Chain: "F" Number of atoms: 6370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 841, 6370 Classifications: {'peptide': 841} Link IDs: {'PTRANS': 24, 'TRANS': 816} Chain breaks: 3 Chain: "D" Number of atoms: 6369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 841, 6369 Classifications: {'peptide': 841} Link IDs: {'PTRANS': 24, 'TRANS': 816} Chain breaks: 3 Chain: "C" Number of atoms: 1068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1068 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 7, 'TRANS': 133} Chain: "G" Number of atoms: 1091 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1091 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 7, 'TRANS': 135} Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "2" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 33 Unusual residues: {' CA': 5, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 51 Unusual residues: {' CA': 9, 'NAG': 3} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 51 Unusual residues: {' CA': 9, 'NAG': 3} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Time building chain proxies: 12.70, per 1000 atoms: 0.55 Number of scatterers: 22949 At special positions: 0 Unit cell: (138.03, 135.89, 173.34, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 2 26.01 Ca 23 19.99 S 218 16.00 O 4423 8.00 N 4085 7.00 C 14198 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=93, symmetry=0 Simple disulfide: pdb=" SG CYS 2 52 " - pdb=" SG CYS 2 86 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 90 " - pdb=" SG CYS 2 207 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 250 " - pdb=" SG CYS 2 281 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 292 " - pdb=" SG CYS 2 322 " distance=2.03 Simple disulfide: pdb=" SG CYS E 275 " - pdb=" SG CYS E 309 " distance=2.03 Simple disulfide: pdb=" SG CYS E 291 " - pdb=" SG CYS E 355 " distance=2.03 Simple disulfide: pdb=" SG CYS E 304 " - pdb=" SG CYS E 365 " distance=2.03 Simple disulfide: pdb=" SG CYS E 335 " - pdb=" SG CYS E 345 " distance=2.03 Simple disulfide: pdb=" SG CYS E 382 " - pdb=" SG CYS E 416 " distance=2.03 Simple disulfide: pdb=" SG CYS E 398 " - pdb=" SG CYS E 462 " distance=2.03 Simple disulfide: pdb=" SG CYS E 411 " - pdb=" SG CYS E 472 " distance=2.03 Simple disulfide: pdb=" SG CYS E 442 " - pdb=" SG CYS E 452 " distance=2.03 Simple disulfide: pdb=" SG CYS E 487 " - pdb=" SG CYS E 521 " distance=2.03 Simple disulfide: pdb=" SG CYS E 503 " - pdb=" SG CYS E 567 " distance=2.03 Simple disulfide: pdb=" SG CYS E 516 " - pdb=" SG CYS E 577 " distance=2.03 Simple disulfide: pdb=" SG CYS E 547 " - pdb=" SG CYS E 557 " distance=2.03 Simple disulfide: pdb=" SG CYS E 592 " - pdb=" SG CYS E 626 " distance=2.03 Simple disulfide: pdb=" SG CYS E 608 " - pdb=" SG CYS E 672 " distance=2.03 Simple disulfide: pdb=" SG CYS E 621 " - pdb=" SG CYS E 682 " distance=2.03 Simple disulfide: pdb=" SG CYS E 652 " - pdb=" SG CYS E 662 " distance=2.03 Simple disulfide: pdb=" SG CYS E 728 " - pdb=" SG CYS E 762 " distance=2.03 Simple disulfide: pdb=" SG CYS E 744 " - pdb=" SG CYS E 808 " distance=2.03 Simple disulfide: pdb=" SG CYS E 757 " - pdb=" SG CYS E 818 " distance=2.03 Simple disulfide: pdb=" SG CYS E 788 " - pdb=" SG CYS E 798 " distance=2.03 Simple disulfide: pdb=" SG CYS E 835 " - pdb=" SG CYS E 869 " distance=2.03 Simple disulfide: pdb=" SG CYS E 864 " - pdb=" SG CYS E 925 " distance=2.03 Simple disulfide: pdb=" SG CYS E 895 " - pdb=" SG CYS E 905 " distance=2.03 Simple disulfide: pdb=" SG CYS E 938 " - pdb=" SG CYS E 972 " distance=2.03 Simple disulfide: pdb=" SG CYS E 954 " - pdb=" SG CYS E1018 " distance=2.03 Simple disulfide: pdb=" SG CYS E 967 " - pdb=" SG CYS E1028 " distance=2.03 Simple disulfide: pdb=" SG CYS E 998 " - pdb=" SG CYS E1008 " distance=2.03 Simple disulfide: pdb=" SG CYS F 168 " - pdb=" SG CYS F 202 " distance=2.03 Simple disulfide: pdb=" SG CYS F 184 " - pdb=" SG CYS F 248 " distance=2.03 Simple disulfide: pdb=" SG CYS F 197 " - pdb=" SG CYS F 258 " distance=2.03 Simple disulfide: pdb=" SG CYS F 228 " - pdb=" SG CYS F 238 " distance=2.03 Simple disulfide: pdb=" SG CYS F 275 " - pdb=" SG CYS F 309 " distance=2.03 Simple disulfide: pdb=" SG CYS F 291 " - pdb=" SG CYS F 355 " distance=2.03 Simple disulfide: pdb=" SG CYS F 304 " - pdb=" SG CYS F 365 " distance=2.03 Simple disulfide: pdb=" SG CYS F 335 " - pdb=" SG CYS F 345 " distance=2.03 Simple disulfide: pdb=" SG CYS F 382 " - pdb=" SG CYS F 416 " distance=2.02 Simple disulfide: pdb=" SG CYS F 398 " - pdb=" SG CYS F 462 " distance=2.03 Simple disulfide: pdb=" SG CYS F 411 " - pdb=" SG CYS F 472 " distance=2.03 Simple disulfide: pdb=" SG CYS F 442 " - pdb=" SG CYS F 452 " distance=2.03 Simple disulfide: pdb=" SG CYS F 487 " - pdb=" SG CYS F 521 " distance=2.03 Simple disulfide: pdb=" SG CYS F 503 " - pdb=" SG CYS F 567 " distance=2.03 Simple disulfide: pdb=" SG CYS F 516 " - pdb=" SG CYS F 577 " distance=2.03 Simple disulfide: pdb=" SG CYS F 547 " - pdb=" SG CYS F 557 " distance=2.03 Simple disulfide: pdb=" SG CYS F 592 " - pdb=" SG CYS F 626 " distance=2.03 Simple disulfide: pdb=" SG CYS F 608 " - pdb=" SG CYS F 672 " distance=2.03 Simple disulfide: pdb=" SG CYS F 621 " - pdb=" SG CYS F 682 " distance=2.03 Simple disulfide: pdb=" SG CYS F 652 " - pdb=" SG CYS F 662 " distance=2.03 Simple disulfide: pdb=" SG CYS F 728 " - pdb=" SG CYS F 762 " distance=2.03 Simple disulfide: pdb=" SG CYS F 744 " - pdb=" SG CYS F 808 " distance=2.03 Simple disulfide: pdb=" SG CYS F 757 " - pdb=" SG CYS F 818 " distance=2.03 Simple disulfide: pdb=" SG CYS F 788 " - pdb=" SG CYS F 798 " distance=2.03 Simple disulfide: pdb=" SG CYS F 835 " - pdb=" SG CYS F 869 " distance=2.03 Simple disulfide: pdb=" SG CYS F 864 " - pdb=" SG CYS F 925 " distance=2.03 Simple disulfide: pdb=" SG CYS F 895 " - pdb=" SG CYS F 905 " distance=2.03 Simple disulfide: pdb=" SG CYS F 938 " - pdb=" SG CYS F 972 " distance=2.03 Simple disulfide: pdb=" SG CYS F 954 " - pdb=" SG CYS F1018 " distance=2.03 Simple disulfide: pdb=" SG CYS F 967 " - pdb=" SG CYS F1028 " distance=2.03 Simple disulfide: pdb=" SG CYS F 998 " - pdb=" SG CYS F1008 " distance=2.03 Simple disulfide: pdb=" SG CYS D 168 " - pdb=" SG CYS D 202 " distance=2.03 Simple disulfide: pdb=" SG CYS D 184 " - pdb=" SG CYS D 248 " distance=2.03 Simple disulfide: pdb=" SG CYS D 197 " - pdb=" SG CYS D 258 " distance=2.03 Simple disulfide: pdb=" SG CYS D 228 " - pdb=" SG CYS D 238 " distance=2.03 Simple disulfide: pdb=" SG CYS D 275 " - pdb=" SG CYS D 309 " distance=2.03 Simple disulfide: pdb=" SG CYS D 291 " - pdb=" SG CYS D 355 " distance=2.03 Simple disulfide: pdb=" SG CYS D 304 " - pdb=" SG CYS D 365 " distance=2.03 Simple disulfide: pdb=" SG CYS D 335 " - pdb=" SG CYS D 345 " distance=2.03 Simple disulfide: pdb=" SG CYS D 382 " - pdb=" SG CYS D 416 " distance=2.03 Simple disulfide: pdb=" SG CYS D 398 " - pdb=" SG CYS D 462 " distance=2.03 Simple disulfide: pdb=" SG CYS D 411 " - pdb=" SG CYS D 472 " distance=2.01 Simple disulfide: pdb=" SG CYS D 442 " - pdb=" SG CYS D 452 " distance=2.03 Simple disulfide: pdb=" SG CYS D 487 " - pdb=" SG CYS D 521 " distance=2.03 Simple disulfide: pdb=" SG CYS D 503 " - pdb=" SG CYS D 567 " distance=2.03 Simple disulfide: pdb=" SG CYS D 516 " - pdb=" SG CYS D 577 " distance=2.03 Simple disulfide: pdb=" SG CYS D 547 " - pdb=" SG CYS D 557 " distance=2.03 Simple disulfide: pdb=" SG CYS D 592 " - pdb=" SG CYS D 626 " distance=2.03 Simple disulfide: pdb=" SG CYS D 608 " - pdb=" SG CYS D 672 " distance=2.03 Simple disulfide: pdb=" SG CYS D 621 " - pdb=" SG CYS D 682 " distance=2.03 Simple disulfide: pdb=" SG CYS D 652 " - pdb=" SG CYS D 662 " distance=2.03 Simple disulfide: pdb=" SG CYS D 728 " - pdb=" SG CYS D 762 " distance=2.03 Simple disulfide: pdb=" SG CYS D 744 " - pdb=" SG CYS D 808 " distance=2.02 Simple disulfide: pdb=" SG CYS D 757 " - pdb=" SG CYS D 818 " distance=2.03 Simple disulfide: pdb=" SG CYS D 788 " - pdb=" SG CYS D 798 " distance=2.03 Simple disulfide: pdb=" SG CYS D 835 " - pdb=" SG CYS D 869 " distance=2.03 Simple disulfide: pdb=" SG CYS D 864 " - pdb=" SG CYS D 925 " distance=2.03 Simple disulfide: pdb=" SG CYS D 895 " - pdb=" SG CYS D 905 " distance=2.03 Simple disulfide: pdb=" SG CYS D 938 " - pdb=" SG CYS D 972 " distance=2.03 Simple disulfide: pdb=" SG CYS D 954 " - pdb=" SG CYS D1018 " distance=2.03 Simple disulfide: pdb=" SG CYS D 967 " - pdb=" SG CYS D1028 " distance=2.03 Simple disulfide: pdb=" SG CYS D 998 " - pdb=" SG CYS D1008 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Links applied BETA1-4 " NAG A 1 " - " NAG A 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " NAG-ASN " NAG 2 401 " - " ASN 2 125 " " NAG 2 402 " - " ASN 2 182 " " NAG A 1 " - " ASN 2 148 " " NAG D1101 " - " ASN D 445 " " NAG D1102 " - " ASN D 767 " " NAG D1103 " - " ASN D1027 " " NAG E1101 " - " ASN E 767 " " NAG E1102 " - " ASN E1027 " " NAG F1101 " - " ASN F 445 " " NAG F1102 " - " ASN F 767 " " NAG F1103 " - " ASN F1027 " " NAG X 1 " - " ASN F 320 " " NAG Y 1 " - " ASN D 320 " Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 5.40 Conformation dependent library (CDL) restraints added in 2.7 seconds 5868 Ramachandran restraints generated. 2934 Oldfield, 0 Emsley, 2934 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5268 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 55 sheets defined 24.1% alpha, 28.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.47 Creating SS restraints... Processing helix chain '2' and resid 141 through 146 Processing helix chain '2' and resid 157 through 162 removed outlier: 4.009A pdb=" N THR 2 161 " --> pdb=" O ASP 2 157 " (cutoff:3.500A) Processing helix chain '2' and resid 246 through 255 Processing helix chain '2' and resid 333 through 346 removed outlier: 4.517A pdb=" N ASP 2 338 " --> pdb=" O THR 2 334 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N TRP 2 339 " --> pdb=" O SER 2 335 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLU 2 346 " --> pdb=" O LYS 2 342 " (cutoff:3.500A) Processing helix chain 'E' and resid 296 through 308 Processing helix chain 'E' and resid 356 through 360 removed outlier: 3.542A pdb=" N GLU E 359 " --> pdb=" O ASN E 356 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ASP E 360 " --> pdb=" O HIS E 357 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 356 through 360' Processing helix chain 'E' and resid 403 through 415 Processing helix chain 'E' and resid 448 through 452 Processing helix chain 'E' and resid 474 through 476 No H-bonds generated for 'chain 'E' and resid 474 through 476' Processing helix chain 'E' and resid 503 through 507 removed outlier: 4.057A pdb=" N PHE E 507 " --> pdb=" O ASP E 504 " (cutoff:3.500A) Processing helix chain 'E' and resid 508 through 519 Processing helix chain 'E' and resid 568 through 572 Processing helix chain 'E' and resid 613 through 624 Processing helix chain 'E' and resid 749 through 760 Processing helix chain 'E' and resid 794 through 798 Processing helix chain 'E' and resid 809 through 813 removed outlier: 3.675A pdb=" N GLU E 812 " --> pdb=" O ARG E 809 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASP E 813 " --> pdb=" O HIS E 810 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 809 through 813' Processing helix chain 'E' and resid 856 through 867 Processing helix chain 'E' and resid 901 through 905 Processing helix chain 'E' and resid 959 through 971 Processing helix chain 'E' and resid 1004 through 1008 Processing helix chain 'E' and resid 1019 through 1023 removed outlier: 3.732A pdb=" N ASP E1023 " --> pdb=" O HIS E1020 " (cutoff:3.500A) Processing helix chain 'F' and resid 189 through 200 Processing helix chain 'F' and resid 249 through 253 removed outlier: 3.805A pdb=" N ASP F 253 " --> pdb=" O HIS F 250 " (cutoff:3.500A) Processing helix chain 'F' and resid 296 through 308 Processing helix chain 'F' and resid 341 through 345 removed outlier: 3.717A pdb=" N GLN F 344 " --> pdb=" O ALA F 341 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N CYS F 345 " --> pdb=" O ILE F 342 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 341 through 345' Processing helix chain 'F' and resid 356 through 360 Processing helix chain 'F' and resid 403 through 415 removed outlier: 3.557A pdb=" N VAL F 409 " --> pdb=" O LYS F 405 " (cutoff:3.500A) Processing helix chain 'F' and resid 504 through 507 removed outlier: 3.863A pdb=" N PHE F 507 " --> pdb=" O ASP F 504 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 504 through 507' Processing helix chain 'F' and resid 508 through 519 Processing helix chain 'F' and resid 568 through 572 removed outlier: 3.539A pdb=" N ASP F 572 " --> pdb=" O HIS F 569 " (cutoff:3.500A) Processing helix chain 'F' and resid 613 through 624 Processing helix chain 'F' and resid 749 through 760 Processing helix chain 'F' and resid 809 through 813 removed outlier: 3.691A pdb=" N ASP F 813 " --> pdb=" O HIS F 810 " (cutoff:3.500A) Processing helix chain 'F' and resid 856 through 867 Processing helix chain 'F' and resid 901 through 905 removed outlier: 3.715A pdb=" N GLN F 904 " --> pdb=" O THR F 901 " (cutoff:3.500A) Processing helix chain 'F' and resid 916 through 920 removed outlier: 3.560A pdb=" N GLU F 920 " --> pdb=" O PRO F 917 " (cutoff:3.500A) Processing helix chain 'F' and resid 959 through 971 removed outlier: 3.511A pdb=" N ALA F 963 " --> pdb=" O ASP F 959 " (cutoff:3.500A) Processing helix chain 'F' and resid 1019 through 1023 removed outlier: 3.565A pdb=" N GLU F1022 " --> pdb=" O GLY F1019 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ASP F1023 " --> pdb=" O HIS F1020 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 1019 through 1023' Processing helix chain 'D' and resid 189 through 200 Processing helix chain 'D' and resid 234 through 238 removed outlier: 3.542A pdb=" N CYS D 238 " --> pdb=" O LEU D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 263 Processing helix chain 'D' and resid 296 through 308 Processing helix chain 'D' and resid 356 through 360 removed outlier: 3.508A pdb=" N ASP D 360 " --> pdb=" O HIS D 357 " (cutoff:3.500A) Processing helix chain 'D' and resid 403 through 415 Processing helix chain 'D' and resid 448 through 452 Processing helix chain 'D' and resid 504 through 507 removed outlier: 4.057A pdb=" N PHE D 507 " --> pdb=" O ASP D 504 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 504 through 507' Processing helix chain 'D' and resid 508 through 519 Processing helix chain 'D' and resid 553 through 557 Processing helix chain 'D' and resid 568 through 572 Processing helix chain 'D' and resid 613 through 624 removed outlier: 3.586A pdb=" N ALA D 617 " --> pdb=" O ASP D 613 " (cutoff:3.500A) Processing helix chain 'D' and resid 749 through 760 removed outlier: 3.707A pdb=" N VAL D 755 " --> pdb=" O SER D 751 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N VAL D 756 " --> pdb=" O ASP D 752 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU D 760 " --> pdb=" O VAL D 756 " (cutoff:3.500A) Processing helix chain 'D' and resid 794 through 798 removed outlier: 3.592A pdb=" N CYS D 798 " --> pdb=" O ILE D 795 " (cutoff:3.500A) Processing helix chain 'D' and resid 809 through 813 Processing helix chain 'D' and resid 856 through 868 Processing helix chain 'D' and resid 901 through 905 removed outlier: 3.778A pdb=" N GLN D 904 " --> pdb=" O THR D 901 " (cutoff:3.500A) Processing helix chain 'D' and resid 959 through 971 Processing helix chain 'D' and resid 1019 through 1023 removed outlier: 3.599A pdb=" N ASP D1023 " --> pdb=" O HIS D1020 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 18 Processing helix chain 'C' and resid 20 through 36 Processing helix chain 'C' and resid 37 through 43 removed outlier: 3.609A pdb=" N THR C 41 " --> pdb=" O THR C 38 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N TYR C 42 " --> pdb=" O THR C 39 " (cutoff:3.500A) Processing helix chain 'C' and resid 52 through 72 Processing helix chain 'C' and resid 75 through 80 Processing helix chain 'C' and resid 80 through 90 Processing helix chain 'C' and resid 94 through 113 removed outlier: 3.693A pdb=" N PHE C 98 " --> pdb=" O ASP C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 138 Processing helix chain 'G' and resid 4 through 17 removed outlier: 4.014A pdb=" N LYS G 17 " --> pdb=" O ALA G 13 " (cutoff:3.500A) Processing helix chain 'G' and resid 19 through 35 removed outlier: 4.217A pdb=" N GLY G 24 " --> pdb=" O VAL G 20 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N GLY G 25 " --> pdb=" O ASP G 21 " (cutoff:3.500A) Processing helix chain 'G' and resid 36 through 46 removed outlier: 3.813A pdb=" N GLU G 43 " --> pdb=" O ARG G 40 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N SER G 44 " --> pdb=" O PHE G 41 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N GLY G 46 " --> pdb=" O GLU G 43 " (cutoff:3.500A) Processing helix chain 'G' and resid 50 through 56 Processing helix chain 'G' and resid 57 through 77 Processing helix chain 'G' and resid 80 through 95 removed outlier: 3.834A pdb=" N THR G 84 " --> pdb=" O ASN G 80 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N THR G 87 " --> pdb=" O GLY G 83 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N LEU G 88 " --> pdb=" O THR G 84 " (cutoff:3.500A) Processing helix chain 'G' and resid 99 through 119 removed outlier: 3.954A pdb=" N PHE G 103 " --> pdb=" O ASP G 99 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ARG G 104 " --> pdb=" O PRO G 100 " (cutoff:3.500A) Processing helix chain 'G' and resid 120 through 122 No H-bonds generated for 'chain 'G' and resid 120 through 122' Processing helix chain 'G' and resid 123 through 141 Processing sheet with id=AA1, first strand: chain '2' and resid 56 through 57 Processing sheet with id=AA2, first strand: chain '2' and resid 170 through 172 removed outlier: 4.158A pdb=" N LEU 2 164 " --> pdb=" O VAL 2 172 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain '2' and resid 238 through 243 removed outlier: 7.705A pdb=" N VAL 2 219 " --> pdb=" O HIS 2 303 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N HIS 2 303 " --> pdb=" O VAL 2 219 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N SER 2 223 " --> pdb=" O ALA 2 299 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N ALA 2 299 " --> pdb=" O SER 2 223 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLY 2 314 " --> pdb=" O PHE 2 300 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N VAL 2 302 " --> pdb=" O ALA 2 312 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N ALA 2 312 " --> pdb=" O VAL 2 302 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N ASP 2 304 " --> pdb=" O TRP 2 310 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N TRP 2 310 " --> pdb=" O ASP 2 304 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N VAL 2 329 " --> pdb=" O SER 2 317 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 266 through 273 removed outlier: 4.084A pdb=" N GLY E 271 " --> pdb=" O SER E 276 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N SER E 276 " --> pdb=" O GLY E 271 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N THR E 364 " --> pdb=" O ALA E 315 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 266 through 273 removed outlier: 4.084A pdb=" N GLY E 271 " --> pdb=" O SER E 276 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N SER E 276 " --> pdb=" O GLY E 271 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N HIS E 327 " --> pdb=" O TRP E 287 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 371 through 377 removed outlier: 7.027A pdb=" N THR E 471 " --> pdb=" O LEU E 420 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 396 through 397 removed outlier: 6.958A pdb=" N LYS E 396 " --> pdb=" O LEU E 437 " (cutoff:3.500A) removed outlier: 8.378A pdb=" N LEU E 439 " --> pdb=" O LYS E 396 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 477 through 481 removed outlier: 4.033A pdb=" N THR E 498 " --> pdb=" O HIS E 495 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 477 through 481 Processing sheet with id=AB1, first strand: chain 'E' and resid 544 through 545 Processing sheet with id=AB2, first strand: chain 'E' and resid 583 through 586 Processing sheet with id=AB3, first strand: chain 'E' and resid 583 through 586 removed outlier: 6.918A pdb=" N ILE E 681 " --> pdb=" O LEU E 630 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 649 through 650 Processing sheet with id=AB5, first strand: chain 'E' and resid 719 through 722 Processing sheet with id=AB6, first strand: chain 'E' and resid 719 through 722 removed outlier: 6.047A pdb=" N GLY E 815 " --> pdb=" O ALA E 768 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N ALA E 768 " --> pdb=" O GLY E 815 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ILE E 817 " --> pdb=" O ILE E 766 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 823 through 827 removed outlier: 3.935A pdb=" N TRP E 922 " --> pdb=" O ASN E 876 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LYS E 874 " --> pdb=" O THR E 924 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 823 through 827 removed outlier: 6.437A pdb=" N LEU E 839 " --> pdb=" O VAL E 850 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N TRP E 889 " --> pdb=" O TRP E 847 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N THR E 849 " --> pdb=" O TRP E 889 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 930 through 932 removed outlier: 6.849A pdb=" N ASN E1027 " --> pdb=" O LEU E 976 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 930 through 932 removed outlier: 5.975A pdb=" N VAL E 942 " --> pdb=" O VAL E 953 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL E 953 " --> pdb=" O VAL E 942 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N TRP E 992 " --> pdb=" O TRP E 950 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N THR E 952 " --> pdb=" O TRP E 992 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 159 through 162 Processing sheet with id=AC3, first strand: chain 'F' and resid 159 through 162 Processing sheet with id=AC4, first strand: chain 'F' and resid 265 through 269 removed outlier: 3.723A pdb=" N SER F 265 " --> pdb=" O ARG F 282 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 265 through 269 removed outlier: 3.723A pdb=" N SER F 265 " --> pdb=" O ARG F 282 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N LEU F 279 " --> pdb=" O ILE F 290 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ILE F 290 " --> pdb=" O LEU F 279 " (cutoff:3.500A) removed outlier: 10.629A pdb=" N TRP F 287 " --> pdb=" O ILE F 328 " (cutoff:3.500A) removed outlier: 9.541A pdb=" N LEU F 330 " --> pdb=" O TRP F 287 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N THR F 289 " --> pdb=" O LEU F 330 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 371 through 377 removed outlier: 6.858A pdb=" N THR F 471 " --> pdb=" O LEU F 420 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 371 through 377 removed outlier: 6.000A pdb=" N VAL F 386 " --> pdb=" O VAL F 397 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N LEU F 437 " --> pdb=" O LEU F 394 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N LYS F 396 " --> pdb=" O LEU F 437 " (cutoff:3.500A) removed outlier: 8.458A pdb=" N LEU F 439 " --> pdb=" O LYS F 396 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 477 through 481 Processing sheet with id=AC9, first strand: chain 'F' and resid 477 through 481 removed outlier: 6.324A pdb=" N VAL F 491 " --> pdb=" O ILE F 502 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ILE F 502 " --> pdb=" O VAL F 491 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N THR F 498 " --> pdb=" O HIS F 495 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N TRP F 541 " --> pdb=" O TRP F 499 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N SER F 501 " --> pdb=" O TRP F 541 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 543 through 545 Processing sheet with id=AD2, first strand: chain 'F' and resid 583 through 586 removed outlier: 6.826A pdb=" N ILE F 681 " --> pdb=" O LEU F 630 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 583 through 586 removed outlier: 6.207A pdb=" N VAL F 596 " --> pdb=" O LEU F 607 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU F 607 " --> pdb=" O VAL F 596 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N TRP F 646 " --> pdb=" O TRP F 604 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N SER F 606 " --> pdb=" O TRP F 646 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 649 through 650 Processing sheet with id=AD5, first strand: chain 'F' and resid 719 through 722 removed outlier: 6.012A pdb=" N GLY F 815 " --> pdb=" O ALA F 768 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N ALA F 768 " --> pdb=" O GLY F 815 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ILE F 817 " --> pdb=" O ILE F 766 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 719 through 722 removed outlier: 14.862A pdb=" N GLY F 730 " --> pdb=" O ASP F 745 " (cutoff:3.500A) removed outlier: 11.135A pdb=" N ASP F 745 " --> pdb=" O GLY F 730 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N VAL F 732 " --> pdb=" O ILE F 743 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ILE F 743 " --> pdb=" O VAL F 732 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N ILE F 781 " --> pdb=" O TRP F 740 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N THR F 742 " --> pdb=" O ILE F 781 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N LEU F 783 " --> pdb=" O THR F 742 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N GLU F 785 " --> pdb=" O CYS F 744 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N ASP F 746 " --> pdb=" O GLU F 785 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 823 through 827 removed outlier: 3.694A pdb=" N TRP F 922 " --> pdb=" O ASN F 876 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'F' and resid 823 through 827 removed outlier: 6.566A pdb=" N LEU F 839 " --> pdb=" O VAL F 850 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL F 850 " --> pdb=" O LEU F 839 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N TRP F 889 " --> pdb=" O TRP F 847 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N THR F 849 " --> pdb=" O TRP F 889 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 929 through 932 removed outlier: 6.204A pdb=" N VAL F 942 " --> pdb=" O VAL F 953 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N VAL F 953 " --> pdb=" O VAL F 942 " (cutoff:3.500A) removed outlier: 10.575A pdb=" N TRP F 950 " --> pdb=" O ILE F 991 " (cutoff:3.500A) removed outlier: 9.486A pdb=" N LEU F 993 " --> pdb=" O TRP F 950 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N THR F 952 " --> pdb=" O LEU F 993 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'F' and resid 929 through 932 Processing sheet with id=AE2, first strand: chain 'D' and resid 159 through 162 Processing sheet with id=AE3, first strand: chain 'D' and resid 159 through 162 Processing sheet with id=AE4, first strand: chain 'D' and resid 265 through 269 removed outlier: 3.696A pdb=" N SER D 265 " --> pdb=" O ARG D 282 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 265 through 269 removed outlier: 3.696A pdb=" N SER D 265 " --> pdb=" O ARG D 282 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N LEU D 279 " --> pdb=" O ILE D 290 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ILE D 290 " --> pdb=" O LEU D 279 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N HIS D 327 " --> pdb=" O TRP D 287 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 371 through 380 removed outlier: 5.927A pdb=" N ALA D 383 " --> pdb=" O GLY D 378 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N THR D 471 " --> pdb=" O LEU D 420 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 371 through 380 removed outlier: 5.927A pdb=" N ALA D 383 " --> pdb=" O GLY D 378 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N VAL D 386 " --> pdb=" O VAL D 397 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N VAL D 397 " --> pdb=" O VAL D 386 " (cutoff:3.500A) removed outlier: 8.419A pdb=" N LEU D 437 " --> pdb=" O LEU D 394 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N LYS D 396 " --> pdb=" O LEU D 437 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N LEU D 439 " --> pdb=" O LYS D 396 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N SER D 440 " --> pdb=" O ASN D 454 " (cutoff:3.500A) removed outlier: 8.286A pdb=" N ASN D 454 " --> pdb=" O SER D 440 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 476 through 481 Processing sheet with id=AE9, first strand: chain 'D' and resid 476 through 481 removed outlier: 6.398A pdb=" N VAL D 491 " --> pdb=" O ILE D 502 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ILE D 502 " --> pdb=" O VAL D 491 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLY D 500 " --> pdb=" O VAL D 493 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N THR D 498 " --> pdb=" O HIS D 495 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N TRP D 499 " --> pdb=" O GLN D 539 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N TRP D 541 " --> pdb=" O TRP D 499 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N SER D 501 " --> pdb=" O TRP D 541 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 543 through 545 Processing sheet with id=AF2, first strand: chain 'D' and resid 583 through 586 removed outlier: 7.228A pdb=" N ILE D 681 " --> pdb=" O LEU D 630 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'D' and resid 583 through 586 removed outlier: 5.280A pdb=" N VAL D 596 " --> pdb=" O LEU D 607 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N TRP D 646 " --> pdb=" O TRP D 604 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N SER D 606 " --> pdb=" O TRP D 646 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'D' and resid 649 through 650 Processing sheet with id=AF5, first strand: chain 'D' and resid 719 through 722 Processing sheet with id=AF6, first strand: chain 'D' and resid 719 through 722 Processing sheet with id=AF7, first strand: chain 'D' and resid 823 through 827 removed outlier: 4.158A pdb=" N TRP D 922 " --> pdb=" O ASN D 876 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS D 874 " --> pdb=" O THR D 924 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'D' and resid 823 through 827 removed outlier: 6.227A pdb=" N LEU D 839 " --> pdb=" O VAL D 850 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N TRP D 889 " --> pdb=" O TRP D 847 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N THR D 849 " --> pdb=" O TRP D 889 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'D' and resid 929 through 932 removed outlier: 6.220A pdb=" N VAL D 942 " --> pdb=" O VAL D 953 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N VAL D 953 " --> pdb=" O VAL D 942 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N TRP D 992 " --> pdb=" O TRP D 950 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N THR D 952 " --> pdb=" O TRP D 992 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'D' and resid 929 through 932 872 hydrogen bonds defined for protein. 2352 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 9.86 Time building geometry restraints manager: 6.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.38: 9284 1.38 - 1.55: 13928 1.55 - 1.72: 1 1.72 - 1.89: 247 1.89 - 2.06: 8 Bond restraints: 23468 Sorted by residual: bond pdb=" CA SER D 473 " pdb=" CB SER D 473 " ideal model delta sigma weight residual 1.524 1.472 0.052 1.30e-02 5.92e+03 1.63e+01 bond pdb=" CA SER E 473 " pdb=" CB SER E 473 " ideal model delta sigma weight residual 1.530 1.487 0.043 1.57e-02 4.06e+03 7.57e+00 bond pdb=" N ASP D 745 " pdb=" CA ASP D 745 " ideal model delta sigma weight residual 1.457 1.489 -0.031 1.29e-02 6.01e+03 5.92e+00 bond pdb=" N THR E 471 " pdb=" CA THR E 471 " ideal model delta sigma weight residual 1.464 1.493 -0.030 1.25e-02 6.40e+03 5.64e+00 bond pdb=" CA ALA E 474 " pdb=" CB ALA E 474 " ideal model delta sigma weight residual 1.530 1.492 0.039 1.69e-02 3.50e+03 5.21e+00 ... (remaining 23463 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.98: 31437 1.98 - 3.95: 359 3.95 - 5.93: 29 5.93 - 7.90: 1 7.90 - 9.88: 2 Bond angle restraints: 31828 Sorted by residual: angle pdb=" N HIS D 475 " pdb=" CA HIS D 475 " pdb=" C HIS D 475 " ideal model delta sigma weight residual 110.97 101.63 9.34 1.09e+00 8.42e-01 7.34e+01 angle pdb=" N ALA D 474 " pdb=" CA ALA D 474 " pdb=" C ALA D 474 " ideal model delta sigma weight residual 113.50 103.62 9.88 1.65e+00 3.67e-01 3.58e+01 angle pdb=" C HIS D 475 " pdb=" CA HIS D 475 " pdb=" CB HIS D 475 " ideal model delta sigma weight residual 110.96 116.89 -5.93 1.54e+00 4.22e-01 1.48e+01 angle pdb=" CA SER E 473 " pdb=" C SER E 473 " pdb=" O SER E 473 " ideal model delta sigma weight residual 120.90 117.29 3.61 1.03e+00 9.43e-01 1.23e+01 angle pdb=" CA CYS E 472 " pdb=" C CYS E 472 " pdb=" O CYS E 472 " ideal model delta sigma weight residual 121.88 118.12 3.76 1.13e+00 7.83e-01 1.11e+01 ... (remaining 31823 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 12659 17.88 - 35.76: 1127 35.76 - 53.65: 216 53.65 - 71.53: 45 71.53 - 89.41: 22 Dihedral angle restraints: 14069 sinusoidal: 5804 harmonic: 8265 Sorted by residual: dihedral pdb=" CB CYS F 275 " pdb=" SG CYS F 275 " pdb=" SG CYS F 309 " pdb=" CB CYS F 309 " ideal model delta sinusoidal sigma weight residual 93.00 169.36 -76.36 1 1.00e+01 1.00e-02 7.34e+01 dihedral pdb=" CB CYS E 291 " pdb=" SG CYS E 291 " pdb=" SG CYS E 355 " pdb=" CB CYS E 355 " ideal model delta sinusoidal sigma weight residual 93.00 158.99 -65.99 1 1.00e+01 1.00e-02 5.69e+01 dihedral pdb=" CB CYS D 275 " pdb=" SG CYS D 275 " pdb=" SG CYS D 309 " pdb=" CB CYS D 309 " ideal model delta sinusoidal sigma weight residual -86.00 -138.96 52.96 1 1.00e+01 1.00e-02 3.82e+01 ... (remaining 14066 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 2694 0.050 - 0.099: 595 0.099 - 0.149: 114 0.149 - 0.198: 3 0.198 - 0.248: 1 Chirality restraints: 3407 Sorted by residual: chirality pdb=" C1 NAG X 2 " pdb=" O4 NAG X 1 " pdb=" C2 NAG X 2 " pdb=" O5 NAG X 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.37 -0.03 2.00e-02 2.50e+03 1.98e+00 chirality pdb=" CA PHE F 283 " pdb=" N PHE F 283 " pdb=" C PHE F 283 " pdb=" CB PHE F 283 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.54e+00 chirality pdb=" CA PRO F 591 " pdb=" N PRO F 591 " pdb=" C PRO F 591 " pdb=" CB PRO F 591 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.17 2.00e-01 2.50e+01 7.10e-01 ... (remaining 3404 not shown) Planarity restraints: 4138 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP D 903 " 0.013 2.00e-02 2.50e+03 1.94e-02 9.37e+00 pdb=" CG TRP D 903 " -0.046 2.00e-02 2.50e+03 pdb=" CD1 TRP D 903 " 0.035 2.00e-02 2.50e+03 pdb=" CD2 TRP D 903 " 0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP D 903 " -0.014 2.00e-02 2.50e+03 pdb=" CE2 TRP D 903 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP D 903 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 903 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 903 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP D 903 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP F 903 " 0.012 2.00e-02 2.50e+03 1.73e-02 7.50e+00 pdb=" CG TRP F 903 " -0.040 2.00e-02 2.50e+03 pdb=" CD1 TRP F 903 " 0.033 2.00e-02 2.50e+03 pdb=" CD2 TRP F 903 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP F 903 " -0.011 2.00e-02 2.50e+03 pdb=" CE2 TRP F 903 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP F 903 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 903 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 903 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP F 903 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL F 281 " 0.011 2.00e-02 2.50e+03 2.25e-02 5.07e+00 pdb=" C VAL F 281 " -0.039 2.00e-02 2.50e+03 pdb=" O VAL F 281 " 0.015 2.00e-02 2.50e+03 pdb=" N ARG F 282 " 0.013 2.00e-02 2.50e+03 ... (remaining 4135 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 313 2.60 - 3.18: 19227 3.18 - 3.75: 37612 3.75 - 4.33: 52720 4.33 - 4.90: 86501 Nonbonded interactions: 196373 Sorted by model distance: nonbonded pdb=" OE2 GLU D 812 " pdb="CA CA D1107 " model vdw 2.025 2.510 nonbonded pdb=" OH TYR 2 254 " pdb=" O TYR 2 327 " model vdw 2.088 3.040 nonbonded pdb=" OD1 ASP E 784 " pdb="CA CA E1105 " model vdw 2.163 2.510 nonbonded pdb=" O MET F 786 " pdb="CA CA F1107 " model vdw 2.168 2.510 nonbonded pdb=" OD1 ASP F 749 " pdb="CA CA F1107 " model vdw 2.182 2.510 ... (remaining 196368 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'X' selection = chain 'Y' } ncs_group { reference = (chain 'D' and (resid 154 through 828 or resid 835 through 1030 or resid 1101 th \ rough 1112)) selection = (chain 'F' and (resid 154 through 691 or resid 718 through 1030 or resid 1101 th \ rough 1112)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.39 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.810 Check model and map are aligned: 0.140 Set scattering table: 0.210 Process input model: 52.020 Find NCS groups from input model: 0.860 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.125 23579 Z= 0.151 Angle : 0.527 9.879 32062 Z= 0.296 Chirality : 0.042 0.248 3407 Planarity : 0.003 0.053 4125 Dihedral : 13.857 89.408 8522 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.37 % Favored : 96.52 % Rotamer: Outliers : 0.12 % Allowed : 0.16 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.15), residues: 2934 helix: 1.68 (0.23), residues: 532 sheet: -0.83 (0.26), residues: 401 loop : -0.82 (0.13), residues: 2001 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.001 TRP D 903 HIS 0.007 0.001 HIS C 122 PHE 0.009 0.001 PHE 2 280 TYR 0.013 0.001 TYR 2 221 ARG 0.003 0.000 ARG F 381 Details of bonding type rmsd link_NAG-ASN : bond 0.00237 ( 13) link_NAG-ASN : angle 1.15704 ( 39) link_BETA1-4 : bond 0.00352 ( 3) link_BETA1-4 : angle 1.25924 ( 9) hydrogen bonds : bond 0.21931 ( 765) hydrogen bonds : angle 8.32673 ( 2352) SS BOND : bond 0.00324 ( 93) SS BOND : angle 0.93970 ( 186) covalent geometry : bond 0.00308 (23468) covalent geometry : angle 0.52185 (31828) Misc. bond : bond 0.09347 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5868 Ramachandran restraints generated. 2934 Oldfield, 0 Emsley, 2934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5868 Ramachandran restraints generated. 2934 Oldfield, 0 Emsley, 2934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 497 residues out of total 2433 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 494 time to evaluate : 2.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 156 LYS cc_start: 0.8160 (tttt) cc_final: 0.7829 (tttp) REVERT: 2 184 SER cc_start: 0.8877 (m) cc_final: 0.8516 (p) REVERT: 2 202 ARG cc_start: 0.7740 (mtm-85) cc_final: 0.6935 (mmm160) REVERT: 2 248 ASP cc_start: 0.8031 (m-30) cc_final: 0.7799 (m-30) REVERT: 2 306 GLU cc_start: 0.7361 (mp0) cc_final: 0.6976 (mp0) REVERT: 2 308 ASP cc_start: 0.8519 (t0) cc_final: 0.8150 (t0) REVERT: 2 341 GLN cc_start: 0.7587 (mm110) cc_final: 0.7326 (mt0) REVERT: E 299 ASP cc_start: 0.6206 (m-30) cc_final: 0.5978 (m-30) REVERT: E 442 CYS cc_start: 0.4242 (t) cc_final: 0.3760 (t) REVERT: E 532 HIS cc_start: 0.8508 (t-90) cc_final: 0.8251 (t70) REVERT: E 544 GLU cc_start: 0.7637 (tm-30) cc_final: 0.7240 (tt0) REVERT: E 550 HIS cc_start: 0.7559 (p90) cc_final: 0.7238 (p90) REVERT: E 615 GLU cc_start: 0.7551 (mp0) cc_final: 0.7275 (mp0) REVERT: E 764 GLU cc_start: 0.7954 (mm-30) cc_final: 0.7636 (pt0) REVERT: E 938 CYS cc_start: 0.6522 (m) cc_final: 0.6165 (m) REVERT: E 995 GLU cc_start: 0.7228 (tt0) cc_final: 0.6739 (tm-30) REVERT: E 997 LYS cc_start: 0.7012 (mmtt) cc_final: 0.6230 (mmtt) REVERT: E 999 LYS cc_start: 0.7760 (mmmt) cc_final: 0.7387 (mmtt) REVERT: F 167 MET cc_start: 0.5833 (mmp) cc_final: 0.5542 (ttp) REVERT: F 187 ASN cc_start: 0.8639 (t0) cc_final: 0.7812 (t0) REVERT: F 240 HIS cc_start: 0.6341 (p90) cc_final: 0.5484 (p90) REVERT: F 253 ASP cc_start: 0.7111 (m-30) cc_final: 0.6879 (m-30) REVERT: F 446 GLU cc_start: 0.7728 (mp0) cc_final: 0.7335 (mp0) REVERT: F 612 TRP cc_start: 0.7678 (t-100) cc_final: 0.7413 (t-100) REVERT: F 649 MET cc_start: 0.8157 (mtm) cc_final: 0.7827 (mtt) REVERT: F 723 ASN cc_start: 0.7812 (t0) cc_final: 0.7577 (m-40) REVERT: F 859 THR cc_start: 0.7949 (m) cc_final: 0.7691 (p) REVERT: F 922 TRP cc_start: 0.8159 (m100) cc_final: 0.7941 (m100) REVERT: F 1011 ARG cc_start: 0.7849 (ttm-80) cc_final: 0.7620 (ttp-170) REVERT: D 177 GLN cc_start: 0.7286 (mp10) cc_final: 0.7034 (mt0) REVERT: D 245 LYS cc_start: 0.8015 (mptt) cc_final: 0.7815 (tttp) REVERT: D 456 GLN cc_start: 0.8897 (mt0) cc_final: 0.8696 (mt0) REVERT: D 550 HIS cc_start: 0.7838 (p-80) cc_final: 0.7583 (p-80) REVERT: D 825 ARG cc_start: 0.8365 (ptt180) cc_final: 0.8015 (ptt-90) REVERT: D 1004 SER cc_start: 0.8528 (p) cc_final: 0.8267 (t) REVERT: G 9 SER cc_start: 0.8764 (p) cc_final: 0.8486 (p) REVERT: G 132 LYS cc_start: 0.8891 (mtpt) cc_final: 0.8667 (mtpp) outliers start: 3 outliers final: 1 residues processed: 496 average time/residue: 0.3710 time to fit residues: 277.1544 Evaluate side-chains 250 residues out of total 2433 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 249 time to evaluate : 2.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 473 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 249 optimal weight: 6.9990 chunk 223 optimal weight: 0.6980 chunk 124 optimal weight: 0.7980 chunk 76 optimal weight: 3.9990 chunk 150 optimal weight: 1.9990 chunk 119 optimal weight: 1.9990 chunk 231 optimal weight: 0.0470 chunk 89 optimal weight: 3.9990 chunk 140 optimal weight: 0.6980 chunk 172 optimal weight: 5.9990 chunk 267 optimal weight: 1.9990 overall best weight: 0.8480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 327 HIS ** E 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 356 ASN E 475 HIS E 539 GLN E 550 HIS E 723 ASN ** E 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 946 HIS ** F 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 284 GLN F 306 GLN F 464 HIS F 587 ASN ** F 797 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 968 GLN D 475 HIS ** D 736 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 810 HIS D 964 GLN D 986 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.181161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.145174 restraints weight = 28955.812| |-----------------------------------------------------------------------------| r_work (start): 0.3717 rms_B_bonded: 2.17 r_work: 0.3376 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3372 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3372 r_free = 0.3372 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3372 r_free = 0.3372 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.67 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3372 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.1653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.142 23579 Z= 0.167 Angle : 0.572 9.905 32062 Z= 0.301 Chirality : 0.045 0.258 3407 Planarity : 0.004 0.049 4125 Dihedral : 5.950 78.581 3476 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.19 % Favored : 95.74 % Rotamer: Outliers : 1.44 % Allowed : 8.59 % Favored : 89.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.15), residues: 2934 helix: 1.88 (0.23), residues: 532 sheet: -0.93 (0.25), residues: 410 loop : -0.86 (0.13), residues: 1992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 922 HIS 0.008 0.001 HIS F 495 PHE 0.014 0.001 PHE 2 300 TYR 0.018 0.001 TYR 2 183 ARG 0.007 0.001 ARG F 758 Details of bonding type rmsd link_NAG-ASN : bond 0.00249 ( 13) link_NAG-ASN : angle 1.99586 ( 39) link_BETA1-4 : bond 0.00133 ( 3) link_BETA1-4 : angle 1.19204 ( 9) hydrogen bonds : bond 0.04450 ( 765) hydrogen bonds : angle 5.62325 ( 2352) SS BOND : bond 0.00403 ( 93) SS BOND : angle 1.20097 ( 186) covalent geometry : bond 0.00397 (23468) covalent geometry : angle 0.56221 (31828) Misc. bond : bond 0.10400 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5868 Ramachandran restraints generated. 2934 Oldfield, 0 Emsley, 2934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5868 Ramachandran restraints generated. 2934 Oldfield, 0 Emsley, 2934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 2433 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 276 time to evaluate : 2.732 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 202 ARG cc_start: 0.8243 (mtm-85) cc_final: 0.7763 (mmm160) REVERT: 2 308 ASP cc_start: 0.8360 (t0) cc_final: 0.8078 (t0) REVERT: 2 337 GLN cc_start: 0.8197 (tt0) cc_final: 0.7879 (mt0) REVERT: E 299 ASP cc_start: 0.6100 (m-30) cc_final: 0.5740 (m-30) REVERT: E 406 GLU cc_start: 0.7426 (mp0) cc_final: 0.7218 (mp0) REVERT: E 532 HIS cc_start: 0.8561 (t-90) cc_final: 0.8329 (t70) REVERT: E 544 GLU cc_start: 0.7719 (tm-30) cc_final: 0.7051 (tt0) REVERT: E 615 GLU cc_start: 0.7802 (mp0) cc_final: 0.7469 (mp0) REVERT: E 745 ASP cc_start: 0.8663 (p0) cc_final: 0.8287 (p0) REVERT: E 764 GLU cc_start: 0.8162 (mm-30) cc_final: 0.7735 (pt0) REVERT: E 891 ASP cc_start: 0.8475 (t0) cc_final: 0.8240 (t0) REVERT: E 938 CYS cc_start: 0.6602 (m) cc_final: 0.6290 (m) REVERT: E 995 GLU cc_start: 0.7309 (tt0) cc_final: 0.6730 (tm-30) REVERT: E 997 LYS cc_start: 0.6951 (mmtt) cc_final: 0.6249 (mmtt) REVERT: F 167 MET cc_start: 0.6063 (mmp) cc_final: 0.5640 (ttp) REVERT: F 187 ASN cc_start: 0.8734 (t0) cc_final: 0.8072 (t0) REVERT: F 240 HIS cc_start: 0.6473 (p90) cc_final: 0.5803 (p90) REVERT: F 346 LYS cc_start: 0.7426 (mmtm) cc_final: 0.7046 (ptmm) REVERT: F 352 LYS cc_start: 0.7473 (tttm) cc_final: 0.6968 (tmtt) REVERT: F 541 TRP cc_start: 0.8568 (m100) cc_final: 0.8266 (m100) REVERT: F 649 MET cc_start: 0.8261 (mtm) cc_final: 0.7996 (mtt) REVERT: F 914 LEU cc_start: 0.8137 (OUTLIER) cc_final: 0.7859 (mp) REVERT: F 922 TRP cc_start: 0.8201 (m100) cc_final: 0.7693 (m100) REVERT: D 622 GLN cc_start: 0.8536 (tp40) cc_final: 0.8298 (tp40) REVERT: D 740 TRP cc_start: 0.8319 (m100) cc_final: 0.8091 (m100) REVERT: D 825 ARG cc_start: 0.8540 (ptt180) cc_final: 0.8003 (ptt-90) REVERT: D 922 TRP cc_start: 0.8319 (m100) cc_final: 0.8067 (m100) outliers start: 35 outliers final: 20 residues processed: 298 average time/residue: 0.3644 time to fit residues: 170.5995 Evaluate side-chains 245 residues out of total 2433 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 224 time to evaluate : 5.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 163 THR Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain E residue 426 VAL Chi-restraints excluded: chain E residue 466 GLU Chi-restraints excluded: chain E residue 515 LEU Chi-restraints excluded: chain E residue 671 LEU Chi-restraints excluded: chain E residue 690 LEU Chi-restraints excluded: chain E residue 886 ILE Chi-restraints excluded: chain E residue 962 ASP Chi-restraints excluded: chain E residue 1026 VAL Chi-restraints excluded: chain F residue 399 ASP Chi-restraints excluded: chain F residue 739 SER Chi-restraints excluded: chain F residue 756 VAL Chi-restraints excluded: chain F residue 914 LEU Chi-restraints excluded: chain F residue 968 GLN Chi-restraints excluded: chain F residue 1004 SER Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 179 ARG Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 481 VAL Chi-restraints excluded: chain D residue 964 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 30 optimal weight: 10.0000 chunk 81 optimal weight: 1.9990 chunk 236 optimal weight: 9.9990 chunk 221 optimal weight: 0.9980 chunk 156 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 chunk 5 optimal weight: 0.4980 chunk 128 optimal weight: 0.3980 chunk 203 optimal weight: 0.0970 chunk 216 optimal weight: 0.2980 chunk 4 optimal weight: 2.9990 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 353 HIS E 356 ASN E 723 ASN ** F 797 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 475 HIS D 986 GLN G 2 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.184213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.139947 restraints weight = 28894.317| |-----------------------------------------------------------------------------| r_work (start): 0.3630 rms_B_bonded: 2.18 r_work: 0.3416 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3281 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3292 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3292 r_free = 0.3292 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.67 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3292 r_free = 0.3292 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.59 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3292 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.2020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.109 23579 Z= 0.118 Angle : 0.520 8.934 32062 Z= 0.274 Chirality : 0.043 0.174 3407 Planarity : 0.004 0.047 4125 Dihedral : 5.667 78.922 3475 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.34 % Favored : 96.59 % Rotamer: Outliers : 1.81 % Allowed : 11.59 % Favored : 86.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.15), residues: 2934 helix: 2.03 (0.23), residues: 532 sheet: -1.08 (0.25), residues: 357 loop : -0.86 (0.13), residues: 2045 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 796 HIS 0.009 0.001 HIS E 550 PHE 0.012 0.001 PHE 2 300 TYR 0.017 0.001 TYR 2 183 ARG 0.005 0.000 ARG F 376 Details of bonding type rmsd link_NAG-ASN : bond 0.00210 ( 13) link_NAG-ASN : angle 1.35960 ( 39) link_BETA1-4 : bond 0.00671 ( 3) link_BETA1-4 : angle 1.31021 ( 9) hydrogen bonds : bond 0.03531 ( 765) hydrogen bonds : angle 5.01671 ( 2352) SS BOND : bond 0.00231 ( 93) SS BOND : angle 0.90205 ( 186) covalent geometry : bond 0.00277 (23468) covalent geometry : angle 0.51514 (31828) Misc. bond : bond 0.08265 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5868 Ramachandran restraints generated. 2934 Oldfield, 0 Emsley, 2934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5868 Ramachandran restraints generated. 2934 Oldfield, 0 Emsley, 2934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 2433 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 255 time to evaluate : 2.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 202 ARG cc_start: 0.8451 (mtm-85) cc_final: 0.7863 (mmm160) REVERT: 2 308 ASP cc_start: 0.8587 (t0) cc_final: 0.8245 (t0) REVERT: 2 337 GLN cc_start: 0.8395 (tt0) cc_final: 0.8003 (mt0) REVERT: E 299 ASP cc_start: 0.6086 (m-30) cc_final: 0.5667 (m-30) REVERT: E 406 GLU cc_start: 0.7413 (mp0) cc_final: 0.6980 (mm-30) REVERT: E 532 HIS cc_start: 0.8578 (t-90) cc_final: 0.8345 (t70) REVERT: E 544 GLU cc_start: 0.7691 (tm-30) cc_final: 0.7001 (tt0) REVERT: E 615 GLU cc_start: 0.7869 (mp0) cc_final: 0.7490 (mp0) REVERT: E 671 LEU cc_start: 0.8366 (OUTLIER) cc_final: 0.8092 (mm) REVERT: E 745 ASP cc_start: 0.8762 (p0) cc_final: 0.8541 (p0) REVERT: E 764 GLU cc_start: 0.8238 (mm-30) cc_final: 0.7671 (pt0) REVERT: E 938 CYS cc_start: 0.6738 (m) cc_final: 0.6406 (m) REVERT: E 995 GLU cc_start: 0.7427 (tt0) cc_final: 0.7047 (tm-30) REVERT: F 167 MET cc_start: 0.6183 (mmp) cc_final: 0.5656 (ttp) REVERT: F 187 ASN cc_start: 0.8663 (t0) cc_final: 0.7988 (t0) REVERT: F 240 HIS cc_start: 0.6543 (p90) cc_final: 0.5835 (p90) REVERT: F 299 ASP cc_start: 0.7890 (m-30) cc_final: 0.7125 (m-30) REVERT: F 336 GLN cc_start: 0.7741 (mp-120) cc_final: 0.7524 (mp10) REVERT: F 541 TRP cc_start: 0.8672 (m100) cc_final: 0.8345 (m100) REVERT: F 640 LYS cc_start: 0.7103 (ptmt) cc_final: 0.6739 (pptt) REVERT: F 649 MET cc_start: 0.8340 (mtm) cc_final: 0.8133 (mtt) REVERT: F 914 LEU cc_start: 0.8099 (OUTLIER) cc_final: 0.7822 (mp) REVERT: F 922 TRP cc_start: 0.8029 (m100) cc_final: 0.7515 (m-10) REVERT: D 550 HIS cc_start: 0.8126 (p-80) cc_final: 0.7801 (p90) REVERT: D 622 GLN cc_start: 0.8597 (tp40) cc_final: 0.8231 (tp40) REVERT: D 825 ARG cc_start: 0.8664 (ptt180) cc_final: 0.8105 (ptt-90) REVERT: D 922 TRP cc_start: 0.8418 (m100) cc_final: 0.8215 (m100) REVERT: D 1004 SER cc_start: 0.8866 (t) cc_final: 0.7986 (p) REVERT: C 90 LYS cc_start: 0.8770 (tttp) cc_final: 0.8568 (tttp) REVERT: G 14 LEU cc_start: 0.8781 (tp) cc_final: 0.8432 (tp) outliers start: 44 outliers final: 23 residues processed: 283 average time/residue: 0.3378 time to fit residues: 150.9907 Evaluate side-chains 247 residues out of total 2433 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 222 time to evaluate : 2.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 163 THR Chi-restraints excluded: chain 2 residue 178 VAL Chi-restraints excluded: chain E residue 356 ASN Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain E residue 388 VAL Chi-restraints excluded: chain E residue 426 VAL Chi-restraints excluded: chain E residue 466 GLU Chi-restraints excluded: chain E residue 481 VAL Chi-restraints excluded: chain E residue 671 LEU Chi-restraints excluded: chain E residue 962 ASP Chi-restraints excluded: chain E residue 1004 SER Chi-restraints excluded: chain E residue 1026 VAL Chi-restraints excluded: chain F residue 399 ASP Chi-restraints excluded: chain F residue 528 LEU Chi-restraints excluded: chain F residue 739 SER Chi-restraints excluded: chain F residue 752 ASP Chi-restraints excluded: chain F residue 914 LEU Chi-restraints excluded: chain F residue 959 ASP Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 179 ARG Chi-restraints excluded: chain D residue 276 SER Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 470 ILE Chi-restraints excluded: chain D residue 481 VAL Chi-restraints excluded: chain D residue 670 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 123 optimal weight: 0.0870 chunk 142 optimal weight: 1.9990 chunk 140 optimal weight: 5.9990 chunk 213 optimal weight: 0.8980 chunk 90 optimal weight: 4.9990 chunk 237 optimal weight: 3.9990 chunk 166 optimal weight: 0.6980 chunk 186 optimal weight: 0.7980 chunk 10 optimal weight: 0.2980 chunk 287 optimal weight: 3.9990 chunk 112 optimal weight: 1.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 327 HIS E 723 ASN ** F 797 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 968 GLN D 475 HIS G 2 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.181920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.143096 restraints weight = 29154.586| |-----------------------------------------------------------------------------| r_work (start): 0.3671 rms_B_bonded: 2.08 r_work: 0.3403 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3271 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3289 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3289 r_free = 0.3289 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.59 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3289 r_free = 0.3289 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.59 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3289 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.2198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.117 23579 Z= 0.124 Angle : 0.511 9.623 32062 Z= 0.268 Chirality : 0.043 0.337 3407 Planarity : 0.004 0.047 4125 Dihedral : 5.526 78.579 3475 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.85 % Favored : 96.08 % Rotamer: Outliers : 1.97 % Allowed : 12.70 % Favored : 85.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.15), residues: 2934 helix: 2.13 (0.23), residues: 532 sheet: -1.04 (0.26), residues: 340 loop : -0.84 (0.13), residues: 2062 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP F 796 HIS 0.007 0.001 HIS E 550 PHE 0.012 0.001 PHE 2 300 TYR 0.015 0.001 TYR 2 183 ARG 0.003 0.000 ARG E 318 Details of bonding type rmsd link_NAG-ASN : bond 0.00415 ( 13) link_NAG-ASN : angle 2.18320 ( 39) link_BETA1-4 : bond 0.00570 ( 3) link_BETA1-4 : angle 1.32364 ( 9) hydrogen bonds : bond 0.03227 ( 765) hydrogen bonds : angle 4.79606 ( 2352) SS BOND : bond 0.00263 ( 93) SS BOND : angle 0.86128 ( 186) covalent geometry : bond 0.00295 (23468) covalent geometry : angle 0.50237 (31828) Misc. bond : bond 0.08834 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5868 Ramachandran restraints generated. 2934 Oldfield, 0 Emsley, 2934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5868 Ramachandran restraints generated. 2934 Oldfield, 0 Emsley, 2934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2433 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 240 time to evaluate : 2.996 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 202 ARG cc_start: 0.8440 (mtm-85) cc_final: 0.7884 (mmm160) REVERT: 2 308 ASP cc_start: 0.8576 (t0) cc_final: 0.8216 (t0) REVERT: E 299 ASP cc_start: 0.6140 (m-30) cc_final: 0.5735 (m-30) REVERT: E 406 GLU cc_start: 0.7375 (mp0) cc_final: 0.6972 (mm-30) REVERT: E 532 HIS cc_start: 0.8518 (t-90) cc_final: 0.8271 (t70) REVERT: E 544 GLU cc_start: 0.7714 (tm-30) cc_final: 0.7095 (tt0) REVERT: E 615 GLU cc_start: 0.7897 (mp0) cc_final: 0.7510 (mp0) REVERT: E 671 LEU cc_start: 0.8449 (OUTLIER) cc_final: 0.8202 (mm) REVERT: E 745 ASP cc_start: 0.8764 (p0) cc_final: 0.8207 (p0) REVERT: E 764 GLU cc_start: 0.8248 (mm-30) cc_final: 0.7742 (pt0) REVERT: E 938 CYS cc_start: 0.6694 (m) cc_final: 0.6443 (m) REVERT: E 995 GLU cc_start: 0.7402 (tt0) cc_final: 0.6978 (tm-30) REVERT: F 167 MET cc_start: 0.6193 (mmp) cc_final: 0.5729 (ttp) REVERT: F 187 ASN cc_start: 0.8643 (t0) cc_final: 0.7984 (t0) REVERT: F 240 HIS cc_start: 0.6548 (p90) cc_final: 0.5900 (p90) REVERT: F 299 ASP cc_start: 0.7898 (m-30) cc_final: 0.7091 (m-30) REVERT: F 640 LYS cc_start: 0.7096 (ptmt) cc_final: 0.6747 (pptt) REVERT: F 801 HIS cc_start: 0.6960 (m-70) cc_final: 0.6725 (m90) REVERT: F 835 CYS cc_start: 0.6300 (m) cc_final: 0.6061 (m) REVERT: F 922 TRP cc_start: 0.8015 (m100) cc_final: 0.7556 (m-10) REVERT: F 938 CYS cc_start: 0.6862 (m) cc_final: 0.6586 (m) REVERT: D 825 ARG cc_start: 0.8598 (ptt180) cc_final: 0.8095 (ptt-90) REVERT: D 922 TRP cc_start: 0.8533 (m100) cc_final: 0.8227 (m100) REVERT: D 1004 SER cc_start: 0.8716 (t) cc_final: 0.7970 (p) REVERT: G 14 LEU cc_start: 0.8753 (tp) cc_final: 0.8442 (tp) outliers start: 48 outliers final: 31 residues processed: 272 average time/residue: 0.3770 time to fit residues: 164.5229 Evaluate side-chains 248 residues out of total 2433 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 216 time to evaluate : 2.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 163 THR Chi-restraints excluded: chain 2 residue 178 VAL Chi-restraints excluded: chain 2 residue 184 SER Chi-restraints excluded: chain E residue 266 LEU Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain E residue 388 VAL Chi-restraints excluded: chain E residue 426 VAL Chi-restraints excluded: chain E residue 466 GLU Chi-restraints excluded: chain E residue 467 GLU Chi-restraints excluded: chain E residue 671 LEU Chi-restraints excluded: chain E residue 690 LEU Chi-restraints excluded: chain E residue 962 ASP Chi-restraints excluded: chain E residue 1004 SER Chi-restraints excluded: chain E residue 1026 VAL Chi-restraints excluded: chain F residue 399 ASP Chi-restraints excluded: chain F residue 528 LEU Chi-restraints excluded: chain F residue 739 SER Chi-restraints excluded: chain F residue 752 ASP Chi-restraints excluded: chain F residue 959 ASP Chi-restraints excluded: chain F residue 968 GLN Chi-restraints excluded: chain F residue 996 VAL Chi-restraints excluded: chain F residue 1004 SER Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 179 ARG Chi-restraints excluded: chain D residue 276 SER Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 470 ILE Chi-restraints excluded: chain D residue 481 VAL Chi-restraints excluded: chain D residue 567 CYS Chi-restraints excluded: chain D residue 670 SER Chi-restraints excluded: chain D residue 749 ASP Chi-restraints excluded: chain C residue 16 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 36 optimal weight: 4.9990 chunk 280 optimal weight: 0.5980 chunk 283 optimal weight: 4.9990 chunk 100 optimal weight: 0.9990 chunk 193 optimal weight: 0.7980 chunk 178 optimal weight: 3.9990 chunk 59 optimal weight: 0.7980 chunk 275 optimal weight: 1.9990 chunk 274 optimal weight: 0.0870 chunk 24 optimal weight: 2.9990 chunk 182 optimal weight: 1.9990 overall best weight: 0.6560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 327 HIS E 723 ASN ** F 797 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 968 GLN D 475 HIS D 876 ASN G 2 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.181144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.143477 restraints weight = 28861.746| |-----------------------------------------------------------------------------| r_work (start): 0.3696 rms_B_bonded: 2.08 r_work: 0.3393 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3254 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3226 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3226 r_free = 0.3226 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.59 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3226 r_free = 0.3226 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.54 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3226 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.2335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.126 23579 Z= 0.130 Angle : 0.508 9.173 32062 Z= 0.265 Chirality : 0.043 0.242 3407 Planarity : 0.004 0.047 4125 Dihedral : 5.370 77.927 3475 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.78 % Favored : 96.15 % Rotamer: Outliers : 2.34 % Allowed : 13.07 % Favored : 84.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.15), residues: 2934 helix: 2.11 (0.23), residues: 535 sheet: -1.07 (0.26), residues: 356 loop : -0.81 (0.13), residues: 2043 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 796 HIS 0.007 0.001 HIS E 550 PHE 0.011 0.001 PHE 2 300 TYR 0.014 0.001 TYR 2 183 ARG 0.004 0.000 ARG F 376 Details of bonding type rmsd link_NAG-ASN : bond 0.00224 ( 13) link_NAG-ASN : angle 1.69658 ( 39) link_BETA1-4 : bond 0.00252 ( 3) link_BETA1-4 : angle 1.34627 ( 9) hydrogen bonds : bond 0.03125 ( 765) hydrogen bonds : angle 4.66794 ( 2352) SS BOND : bond 0.00257 ( 93) SS BOND : angle 0.99318 ( 186) covalent geometry : bond 0.00313 (23468) covalent geometry : angle 0.49999 (31828) Misc. bond : bond 0.09513 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5868 Ramachandran restraints generated. 2934 Oldfield, 0 Emsley, 2934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5868 Ramachandran restraints generated. 2934 Oldfield, 0 Emsley, 2934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 2433 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 236 time to evaluate : 2.655 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 202 ARG cc_start: 0.8477 (mtm-85) cc_final: 0.7912 (mmm160) REVERT: 2 308 ASP cc_start: 0.8603 (t0) cc_final: 0.8247 (t0) REVERT: E 299 ASP cc_start: 0.6131 (m-30) cc_final: 0.5704 (m-30) REVERT: E 406 GLU cc_start: 0.7398 (mp0) cc_final: 0.7010 (mm-30) REVERT: E 532 HIS cc_start: 0.8507 (t-90) cc_final: 0.8253 (t70) REVERT: E 544 GLU cc_start: 0.7690 (tm-30) cc_final: 0.7054 (tt0) REVERT: E 615 GLU cc_start: 0.7960 (mp0) cc_final: 0.7545 (mp0) REVERT: E 671 LEU cc_start: 0.8498 (OUTLIER) cc_final: 0.8232 (mm) REVERT: E 745 ASP cc_start: 0.8820 (p0) cc_final: 0.8230 (p0) REVERT: E 764 GLU cc_start: 0.8258 (mm-30) cc_final: 0.7758 (pt0) REVERT: E 855 MET cc_start: 0.6867 (tpp) cc_final: 0.6529 (ttm) REVERT: E 995 GLU cc_start: 0.7442 (tt0) cc_final: 0.7205 (tm-30) REVERT: F 167 MET cc_start: 0.6189 (mmp) cc_final: 0.5749 (ttp) REVERT: F 187 ASN cc_start: 0.8631 (t0) cc_final: 0.8005 (t0) REVERT: F 240 HIS cc_start: 0.6701 (p90) cc_final: 0.6006 (p90) REVERT: F 299 ASP cc_start: 0.7911 (m-30) cc_final: 0.7119 (m-30) REVERT: F 801 HIS cc_start: 0.7032 (m-70) cc_final: 0.6826 (m90) REVERT: F 835 CYS cc_start: 0.6533 (m) cc_final: 0.6306 (m) REVERT: F 922 TRP cc_start: 0.8031 (m100) cc_final: 0.7592 (m-10) REVERT: F 938 CYS cc_start: 0.6897 (m) cc_final: 0.6626 (m) REVERT: D 344 GLN cc_start: 0.8367 (OUTLIER) cc_final: 0.6863 (mp10) REVERT: D 550 HIS cc_start: 0.8087 (p-80) cc_final: 0.7848 (p90) REVERT: D 618 HIS cc_start: 0.7439 (m-70) cc_final: 0.6739 (m170) REVERT: D 742 THR cc_start: 0.7377 (OUTLIER) cc_final: 0.7009 (m) REVERT: D 825 ARG cc_start: 0.8638 (ptt180) cc_final: 0.8133 (ptt-90) REVERT: D 1004 SER cc_start: 0.8732 (t) cc_final: 0.8010 (p) REVERT: G 14 LEU cc_start: 0.8780 (tp) cc_final: 0.8505 (tp) outliers start: 57 outliers final: 42 residues processed: 276 average time/residue: 0.3579 time to fit residues: 158.9569 Evaluate side-chains 261 residues out of total 2433 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 216 time to evaluate : 2.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 163 THR Chi-restraints excluded: chain 2 residue 178 VAL Chi-restraints excluded: chain 2 residue 184 SER Chi-restraints excluded: chain 2 residue 259 VAL Chi-restraints excluded: chain 2 residue 324 VAL Chi-restraints excluded: chain 2 residue 331 VAL Chi-restraints excluded: chain E residue 266 LEU Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain E residue 388 VAL Chi-restraints excluded: chain E residue 426 VAL Chi-restraints excluded: chain E residue 466 GLU Chi-restraints excluded: chain E residue 467 GLU Chi-restraints excluded: chain E residue 481 VAL Chi-restraints excluded: chain E residue 671 LEU Chi-restraints excluded: chain E residue 996 VAL Chi-restraints excluded: chain E residue 1004 SER Chi-restraints excluded: chain E residue 1026 VAL Chi-restraints excluded: chain F residue 248 CYS Chi-restraints excluded: chain F residue 363 VAL Chi-restraints excluded: chain F residue 399 ASP Chi-restraints excluded: chain F residue 528 LEU Chi-restraints excluded: chain F residue 628 VAL Chi-restraints excluded: chain F residue 736 HIS Chi-restraints excluded: chain F residue 739 SER Chi-restraints excluded: chain F residue 752 ASP Chi-restraints excluded: chain F residue 959 ASP Chi-restraints excluded: chain F residue 968 GLN Chi-restraints excluded: chain F residue 996 VAL Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 179 ARG Chi-restraints excluded: chain D residue 273 THR Chi-restraints excluded: chain D residue 276 SER Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 344 GLN Chi-restraints excluded: chain D residue 470 ILE Chi-restraints excluded: chain D residue 481 VAL Chi-restraints excluded: chain D residue 567 CYS Chi-restraints excluded: chain D residue 670 SER Chi-restraints excluded: chain D residue 742 THR Chi-restraints excluded: chain D residue 749 ASP Chi-restraints excluded: chain D residue 755 VAL Chi-restraints excluded: chain D residue 876 ASN Chi-restraints excluded: chain C residue 1 VAL Chi-restraints excluded: chain C residue 16 LYS Chi-restraints excluded: chain C residue 113 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 100 optimal weight: 6.9990 chunk 79 optimal weight: 0.9980 chunk 32 optimal weight: 0.0980 chunk 139 optimal weight: 1.9990 chunk 259 optimal weight: 4.9990 chunk 294 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 113 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 175 optimal weight: 0.5980 chunk 220 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 456 GLN E 723 ASN ** F 797 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 968 GLN D 475 HIS D 876 ASN G 2 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.181641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.139887 restraints weight = 28782.928| |-----------------------------------------------------------------------------| r_work (start): 0.3633 rms_B_bonded: 2.22 r_work: 0.3354 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3211 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3211 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3211 r_free = 0.3211 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.54 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3211 r_free = 0.3211 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.53 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3211 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.2459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.144 23579 Z= 0.154 Angle : 0.514 8.829 32062 Z= 0.269 Chirality : 0.043 0.205 3407 Planarity : 0.004 0.047 4125 Dihedral : 5.301 77.865 3475 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.36 % Favored : 95.57 % Rotamer: Outliers : 2.71 % Allowed : 13.28 % Favored : 84.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.15), residues: 2934 helix: 2.06 (0.23), residues: 535 sheet: -1.15 (0.26), residues: 360 loop : -0.82 (0.13), residues: 2039 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 796 HIS 0.007 0.001 HIS E 550 PHE 0.012 0.001 PHE 2 300 TYR 0.014 0.001 TYR 2 239 ARG 0.007 0.000 ARG F 376 Details of bonding type rmsd link_NAG-ASN : bond 0.00180 ( 13) link_NAG-ASN : angle 1.58777 ( 39) link_BETA1-4 : bond 0.00281 ( 3) link_BETA1-4 : angle 1.41566 ( 9) hydrogen bonds : bond 0.03132 ( 765) hydrogen bonds : angle 4.65698 ( 2352) SS BOND : bond 0.00310 ( 93) SS BOND : angle 1.03109 ( 186) covalent geometry : bond 0.00372 (23468) covalent geometry : angle 0.50598 (31828) Misc. bond : bond 0.10768 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5868 Ramachandran restraints generated. 2934 Oldfield, 0 Emsley, 2934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5868 Ramachandran restraints generated. 2934 Oldfield, 0 Emsley, 2934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 2433 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 230 time to evaluate : 2.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 202 ARG cc_start: 0.8525 (mtm-85) cc_final: 0.7918 (mmm160) REVERT: 2 308 ASP cc_start: 0.8720 (t0) cc_final: 0.8368 (t0) REVERT: E 299 ASP cc_start: 0.6126 (m-30) cc_final: 0.5714 (m-30) REVERT: E 406 GLU cc_start: 0.7444 (mp0) cc_final: 0.7005 (mm-30) REVERT: E 466 GLU cc_start: 0.6391 (OUTLIER) cc_final: 0.6065 (pm20) REVERT: E 532 HIS cc_start: 0.8541 (t-90) cc_final: 0.8287 (t70) REVERT: E 544 GLU cc_start: 0.7693 (tm-30) cc_final: 0.7039 (tt0) REVERT: E 615 GLU cc_start: 0.7995 (mp0) cc_final: 0.7543 (mp0) REVERT: E 671 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.8264 (mm) REVERT: E 745 ASP cc_start: 0.8869 (p0) cc_final: 0.8600 (p0) REVERT: E 764 GLU cc_start: 0.8375 (mm-30) cc_final: 0.7823 (pt0) REVERT: E 820 GLU cc_start: 0.8473 (mm-30) cc_final: 0.8092 (mt-10) REVERT: E 855 MET cc_start: 0.6807 (tpp) cc_final: 0.6505 (ttm) REVERT: E 995 GLU cc_start: 0.7659 (tt0) cc_final: 0.7383 (tm-30) REVERT: F 167 MET cc_start: 0.6244 (mmp) cc_final: 0.5784 (ttp) REVERT: F 240 HIS cc_start: 0.6688 (p90) cc_final: 0.5986 (p90) REVERT: F 785 GLU cc_start: 0.7507 (mm-30) cc_final: 0.7040 (mm-30) REVERT: F 801 HIS cc_start: 0.7058 (m-70) cc_final: 0.6820 (m90) REVERT: F 835 CYS cc_start: 0.6627 (m) cc_final: 0.6418 (m) REVERT: F 922 TRP cc_start: 0.8076 (m100) cc_final: 0.7629 (m-10) REVERT: F 938 CYS cc_start: 0.6929 (m) cc_final: 0.6650 (m) REVERT: D 344 GLN cc_start: 0.8410 (OUTLIER) cc_final: 0.6922 (mp10) REVERT: D 550 HIS cc_start: 0.8181 (p-80) cc_final: 0.7874 (p90) REVERT: D 618 HIS cc_start: 0.7405 (m-70) cc_final: 0.6756 (m170) REVERT: D 742 THR cc_start: 0.7408 (OUTLIER) cc_final: 0.7046 (m) REVERT: D 825 ARG cc_start: 0.8669 (ptt180) cc_final: 0.8141 (ptt-90) REVERT: D 1004 SER cc_start: 0.8724 (t) cc_final: 0.8027 (p) REVERT: C 56 LYS cc_start: 0.8136 (tttt) cc_final: 0.7617 (mmtt) REVERT: G 14 LEU cc_start: 0.8730 (tp) cc_final: 0.8492 (tp) outliers start: 66 outliers final: 52 residues processed: 279 average time/residue: 0.3448 time to fit residues: 153.0240 Evaluate side-chains 270 residues out of total 2433 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 214 time to evaluate : 2.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 163 THR Chi-restraints excluded: chain 2 residue 178 VAL Chi-restraints excluded: chain 2 residue 184 SER Chi-restraints excluded: chain 2 residue 259 VAL Chi-restraints excluded: chain 2 residue 324 VAL Chi-restraints excluded: chain 2 residue 331 VAL Chi-restraints excluded: chain E residue 307 LEU Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain E residue 388 VAL Chi-restraints excluded: chain E residue 426 VAL Chi-restraints excluded: chain E residue 466 GLU Chi-restraints excluded: chain E residue 467 GLU Chi-restraints excluded: chain E residue 481 VAL Chi-restraints excluded: chain E residue 485 ILE Chi-restraints excluded: chain E residue 671 LEU Chi-restraints excluded: chain E residue 690 LEU Chi-restraints excluded: chain E residue 760 LEU Chi-restraints excluded: chain E residue 953 VAL Chi-restraints excluded: chain E residue 996 VAL Chi-restraints excluded: chain E residue 1004 SER Chi-restraints excluded: chain E residue 1026 VAL Chi-restraints excluded: chain F residue 248 CYS Chi-restraints excluded: chain F residue 363 VAL Chi-restraints excluded: chain F residue 399 ASP Chi-restraints excluded: chain F residue 443 ASN Chi-restraints excluded: chain F residue 524 VAL Chi-restraints excluded: chain F residue 528 LEU Chi-restraints excluded: chain F residue 628 VAL Chi-restraints excluded: chain F residue 664 VAL Chi-restraints excluded: chain F residue 736 HIS Chi-restraints excluded: chain F residue 739 SER Chi-restraints excluded: chain F residue 752 ASP Chi-restraints excluded: chain F residue 959 ASP Chi-restraints excluded: chain F residue 968 GLN Chi-restraints excluded: chain F residue 996 VAL Chi-restraints excluded: chain F residue 1004 SER Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 179 ARG Chi-restraints excluded: chain D residue 273 THR Chi-restraints excluded: chain D residue 276 SER Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 344 GLN Chi-restraints excluded: chain D residue 470 ILE Chi-restraints excluded: chain D residue 481 VAL Chi-restraints excluded: chain D residue 524 VAL Chi-restraints excluded: chain D residue 567 CYS Chi-restraints excluded: chain D residue 645 ILE Chi-restraints excluded: chain D residue 670 SER Chi-restraints excluded: chain D residue 742 THR Chi-restraints excluded: chain D residue 749 ASP Chi-restraints excluded: chain D residue 755 VAL Chi-restraints excluded: chain D residue 960 LEU Chi-restraints excluded: chain C residue 1 VAL Chi-restraints excluded: chain C residue 16 LYS Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 113 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 172 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 chunk 63 optimal weight: 6.9990 chunk 71 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 chunk 133 optimal weight: 0.9990 chunk 1 optimal weight: 8.9990 chunk 222 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 144 optimal weight: 4.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 569 HIS E 723 ASN F 648 HIS ** F 797 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 475 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.179256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.136148 restraints weight = 28926.214| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 2.11 r_work: 0.3311 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3176 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3221 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3221 r_free = 0.3221 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.53 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3221 r_free = 0.3221 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.61 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3221 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.2663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.174 23579 Z= 0.209 Angle : 0.559 9.211 32062 Z= 0.292 Chirality : 0.045 0.231 3407 Planarity : 0.004 0.050 4125 Dihedral : 5.378 79.017 3475 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.67 % Favored : 95.26 % Rotamer: Outliers : 2.96 % Allowed : 13.77 % Favored : 83.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.15), residues: 2934 helix: 1.82 (0.23), residues: 536 sheet: -1.21 (0.25), residues: 359 loop : -0.89 (0.13), residues: 2039 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP F 796 HIS 0.007 0.001 HIS 2 124 PHE 0.016 0.001 PHE 2 280 TYR 0.015 0.002 TYR 2 239 ARG 0.008 0.000 ARG E 392 Details of bonding type rmsd link_NAG-ASN : bond 0.00222 ( 13) link_NAG-ASN : angle 1.72349 ( 39) link_BETA1-4 : bond 0.00353 ( 3) link_BETA1-4 : angle 1.62952 ( 9) hydrogen bonds : bond 0.03362 ( 765) hydrogen bonds : angle 4.80265 ( 2352) SS BOND : bond 0.00398 ( 93) SS BOND : angle 1.16813 ( 186) covalent geometry : bond 0.00504 (23468) covalent geometry : angle 0.55015 (31828) Misc. bond : bond 0.12866 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5868 Ramachandran restraints generated. 2934 Oldfield, 0 Emsley, 2934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5868 Ramachandran restraints generated. 2934 Oldfield, 0 Emsley, 2934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 2433 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 237 time to evaluate : 3.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 202 ARG cc_start: 0.8481 (mtm-85) cc_final: 0.7878 (mmm160) REVERT: 2 308 ASP cc_start: 0.8746 (t0) cc_final: 0.8467 (t0) REVERT: E 299 ASP cc_start: 0.6161 (m-30) cc_final: 0.5733 (m-30) REVERT: E 376 ARG cc_start: 0.7904 (mmm-85) cc_final: 0.7232 (mtm180) REVERT: E 406 GLU cc_start: 0.7417 (mp0) cc_final: 0.6995 (mm-30) REVERT: E 466 GLU cc_start: 0.6517 (OUTLIER) cc_final: 0.6199 (pm20) REVERT: E 532 HIS cc_start: 0.8588 (t-90) cc_final: 0.8334 (t70) REVERT: E 544 GLU cc_start: 0.7787 (tm-30) cc_final: 0.7076 (tt0) REVERT: E 671 LEU cc_start: 0.8625 (OUTLIER) cc_final: 0.8343 (mm) REVERT: E 745 ASP cc_start: 0.8887 (p0) cc_final: 0.8627 (p0) REVERT: E 764 GLU cc_start: 0.8327 (mm-30) cc_final: 0.7926 (pt0) REVERT: E 820 GLU cc_start: 0.8508 (mm-30) cc_final: 0.8215 (mt-10) REVERT: E 995 GLU cc_start: 0.7653 (tt0) cc_final: 0.7415 (tm-30) REVERT: F 167 MET cc_start: 0.6366 (mmp) cc_final: 0.5924 (ttp) REVERT: F 187 ASN cc_start: 0.8632 (t0) cc_final: 0.7805 (t0) REVERT: F 240 HIS cc_start: 0.6710 (p90) cc_final: 0.6065 (p90) REVERT: F 645 ILE cc_start: 0.7853 (mm) cc_final: 0.7485 (pt) REVERT: F 801 HIS cc_start: 0.7075 (m-70) cc_final: 0.6874 (m90) REVERT: F 903 TRP cc_start: 0.8240 (m-10) cc_final: 0.7826 (m100) REVERT: F 922 TRP cc_start: 0.8113 (m100) cc_final: 0.7774 (m100) REVERT: F 938 CYS cc_start: 0.6776 (m) cc_final: 0.6494 (m) REVERT: D 344 GLN cc_start: 0.8392 (OUTLIER) cc_final: 0.6954 (mp10) REVERT: D 550 HIS cc_start: 0.8224 (p-80) cc_final: 0.7913 (p90) REVERT: D 580 TYR cc_start: 0.8588 (p90) cc_final: 0.8091 (p90) REVERT: D 618 HIS cc_start: 0.7369 (m-70) cc_final: 0.6716 (m170) REVERT: D 742 THR cc_start: 0.7811 (OUTLIER) cc_final: 0.7441 (m) REVERT: D 825 ARG cc_start: 0.8663 (ptt180) cc_final: 0.8016 (ptt-90) REVERT: D 922 TRP cc_start: 0.8526 (m100) cc_final: 0.8154 (m100) REVERT: D 1004 SER cc_start: 0.8760 (t) cc_final: 0.7962 (p) REVERT: C 56 LYS cc_start: 0.8046 (tttt) cc_final: 0.7562 (mmtt) REVERT: C 126 ASP cc_start: 0.8958 (t70) cc_final: 0.8731 (t0) REVERT: G 14 LEU cc_start: 0.8742 (tp) cc_final: 0.8522 (tp) outliers start: 72 outliers final: 54 residues processed: 290 average time/residue: 0.3830 time to fit residues: 179.6934 Evaluate side-chains 281 residues out of total 2433 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 223 time to evaluate : 2.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 95 ASN Chi-restraints excluded: chain 2 residue 163 THR Chi-restraints excluded: chain 2 residue 178 VAL Chi-restraints excluded: chain 2 residue 184 SER Chi-restraints excluded: chain 2 residue 331 VAL Chi-restraints excluded: chain E residue 266 LEU Chi-restraints excluded: chain E residue 426 VAL Chi-restraints excluded: chain E residue 466 GLU Chi-restraints excluded: chain E residue 467 GLU Chi-restraints excluded: chain E residue 481 VAL Chi-restraints excluded: chain E residue 485 ILE Chi-restraints excluded: chain E residue 671 LEU Chi-restraints excluded: chain E residue 690 LEU Chi-restraints excluded: chain E residue 760 LEU Chi-restraints excluded: chain E residue 938 CYS Chi-restraints excluded: chain E residue 949 SER Chi-restraints excluded: chain E residue 953 VAL Chi-restraints excluded: chain E residue 962 ASP Chi-restraints excluded: chain E residue 996 VAL Chi-restraints excluded: chain E residue 1004 SER Chi-restraints excluded: chain E residue 1026 VAL Chi-restraints excluded: chain F residue 248 CYS Chi-restraints excluded: chain F residue 363 VAL Chi-restraints excluded: chain F residue 367 ASP Chi-restraints excluded: chain F residue 399 ASP Chi-restraints excluded: chain F residue 443 ASN Chi-restraints excluded: chain F residue 524 VAL Chi-restraints excluded: chain F residue 528 LEU Chi-restraints excluded: chain F residue 628 VAL Chi-restraints excluded: chain F residue 640 LYS Chi-restraints excluded: chain F residue 664 VAL Chi-restraints excluded: chain F residue 739 SER Chi-restraints excluded: chain F residue 742 THR Chi-restraints excluded: chain F residue 752 ASP Chi-restraints excluded: chain F residue 959 ASP Chi-restraints excluded: chain F residue 968 GLN Chi-restraints excluded: chain F residue 996 VAL Chi-restraints excluded: chain F residue 1004 SER Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 179 ARG Chi-restraints excluded: chain D residue 273 THR Chi-restraints excluded: chain D residue 276 SER Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 344 GLN Chi-restraints excluded: chain D residue 382 CYS Chi-restraints excluded: chain D residue 470 ILE Chi-restraints excluded: chain D residue 481 VAL Chi-restraints excluded: chain D residue 524 VAL Chi-restraints excluded: chain D residue 567 CYS Chi-restraints excluded: chain D residue 645 ILE Chi-restraints excluded: chain D residue 742 THR Chi-restraints excluded: chain D residue 749 ASP Chi-restraints excluded: chain D residue 755 VAL Chi-restraints excluded: chain D residue 996 VAL Chi-restraints excluded: chain C residue 1 VAL Chi-restraints excluded: chain C residue 16 LYS Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 113 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 82 optimal weight: 1.9990 chunk 227 optimal weight: 1.9990 chunk 127 optimal weight: 0.7980 chunk 247 optimal weight: 0.7980 chunk 34 optimal weight: 10.0000 chunk 140 optimal weight: 3.9990 chunk 291 optimal weight: 0.5980 chunk 219 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 30 optimal weight: 0.9990 chunk 147 optimal weight: 7.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 569 HIS E 723 ASN F 611 HIS ** F 797 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 968 GLN D 240 HIS D 475 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.180911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.137701 restraints weight = 28886.122| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 2.25 r_work: 0.3340 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3195 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3193 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3193 r_free = 0.3193 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.61 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3193 r_free = 0.3193 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.56 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3193 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.2734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.132 23579 Z= 0.145 Angle : 0.519 9.153 32062 Z= 0.272 Chirality : 0.043 0.209 3407 Planarity : 0.004 0.048 4125 Dihedral : 5.196 79.332 3475 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.40 % Favored : 95.54 % Rotamer: Outliers : 2.79 % Allowed : 14.59 % Favored : 82.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.15), residues: 2934 helix: 2.02 (0.23), residues: 535 sheet: -1.24 (0.26), residues: 352 loop : -0.85 (0.13), residues: 2047 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP F 796 HIS 0.006 0.001 HIS E 550 PHE 0.012 0.001 PHE 2 300 TYR 0.015 0.001 TYR 2 239 ARG 0.008 0.000 ARG F 376 Details of bonding type rmsd link_NAG-ASN : bond 0.00183 ( 13) link_NAG-ASN : angle 1.57820 ( 39) link_BETA1-4 : bond 0.00239 ( 3) link_BETA1-4 : angle 1.36899 ( 9) hydrogen bonds : bond 0.03085 ( 765) hydrogen bonds : angle 4.63256 ( 2352) SS BOND : bond 0.00284 ( 93) SS BOND : angle 1.01443 ( 186) covalent geometry : bond 0.00350 (23468) covalent geometry : angle 0.51190 (31828) Misc. bond : bond 0.10080 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5868 Ramachandran restraints generated. 2934 Oldfield, 0 Emsley, 2934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5868 Ramachandran restraints generated. 2934 Oldfield, 0 Emsley, 2934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 2433 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 231 time to evaluate : 4.167 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 202 ARG cc_start: 0.8561 (mtm-85) cc_final: 0.7909 (mmm160) REVERT: 2 308 ASP cc_start: 0.8811 (t0) cc_final: 0.8480 (t0) REVERT: E 299 ASP cc_start: 0.6131 (m-30) cc_final: 0.5703 (m-30) REVERT: E 376 ARG cc_start: 0.7934 (mmm-85) cc_final: 0.7220 (mtm180) REVERT: E 406 GLU cc_start: 0.7427 (mp0) cc_final: 0.6859 (mp0) REVERT: E 466 GLU cc_start: 0.6500 (OUTLIER) cc_final: 0.6176 (pm20) REVERT: E 532 HIS cc_start: 0.8611 (t-90) cc_final: 0.8353 (t70) REVERT: E 544 GLU cc_start: 0.7791 (tm-30) cc_final: 0.7058 (tt0) REVERT: E 615 GLU cc_start: 0.8044 (mp0) cc_final: 0.7697 (mp0) REVERT: E 671 LEU cc_start: 0.8617 (OUTLIER) cc_final: 0.8308 (mm) REVERT: E 745 ASP cc_start: 0.8880 (p0) cc_final: 0.8602 (p0) REVERT: E 764 GLU cc_start: 0.8347 (mm-30) cc_final: 0.7837 (pt0) REVERT: E 820 GLU cc_start: 0.8582 (mm-30) cc_final: 0.8268 (mt-10) REVERT: E 855 MET cc_start: 0.7243 (ttm) cc_final: 0.6950 (ttm) REVERT: E 995 GLU cc_start: 0.7695 (tt0) cc_final: 0.7417 (tm-30) REVERT: F 167 MET cc_start: 0.6432 (mmp) cc_final: 0.5916 (ttp) REVERT: F 187 ASN cc_start: 0.8670 (t0) cc_final: 0.7831 (t0) REVERT: F 240 HIS cc_start: 0.6713 (p90) cc_final: 0.6021 (p90) REVERT: F 645 ILE cc_start: 0.7874 (mm) cc_final: 0.7484 (pt) REVERT: F 801 HIS cc_start: 0.7078 (m-70) cc_final: 0.6856 (m90) REVERT: F 903 TRP cc_start: 0.8168 (m-10) cc_final: 0.7915 (m100) REVERT: F 922 TRP cc_start: 0.8146 (m100) cc_final: 0.7854 (m100) REVERT: F 938 CYS cc_start: 0.7005 (m) cc_final: 0.6732 (m) REVERT: D 344 GLN cc_start: 0.8407 (OUTLIER) cc_final: 0.6910 (mp10) REVERT: D 550 HIS cc_start: 0.8247 (p-80) cc_final: 0.7913 (p90) REVERT: D 618 HIS cc_start: 0.7369 (m-70) cc_final: 0.6745 (m170) REVERT: D 736 HIS cc_start: 0.4706 (OUTLIER) cc_final: 0.4208 (p-80) REVERT: D 742 THR cc_start: 0.7831 (OUTLIER) cc_final: 0.7475 (m) REVERT: D 825 ARG cc_start: 0.8657 (ptt180) cc_final: 0.8147 (ptt-90) REVERT: D 922 TRP cc_start: 0.8487 (m100) cc_final: 0.8107 (m100) REVERT: D 1004 SER cc_start: 0.8784 (t) cc_final: 0.7976 (p) REVERT: C 56 LYS cc_start: 0.8081 (tttt) cc_final: 0.7541 (mmtt) outliers start: 68 outliers final: 53 residues processed: 282 average time/residue: 0.4490 time to fit residues: 201.8623 Evaluate side-chains 272 residues out of total 2433 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 214 time to evaluate : 2.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 95 ASN Chi-restraints excluded: chain 2 residue 163 THR Chi-restraints excluded: chain 2 residue 178 VAL Chi-restraints excluded: chain 2 residue 184 SER Chi-restraints excluded: chain 2 residue 331 VAL Chi-restraints excluded: chain E residue 266 LEU Chi-restraints excluded: chain E residue 307 LEU Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain E residue 426 VAL Chi-restraints excluded: chain E residue 448 SER Chi-restraints excluded: chain E residue 466 GLU Chi-restraints excluded: chain E residue 481 VAL Chi-restraints excluded: chain E residue 485 ILE Chi-restraints excluded: chain E residue 523 THR Chi-restraints excluded: chain E residue 671 LEU Chi-restraints excluded: chain E residue 690 LEU Chi-restraints excluded: chain E residue 938 CYS Chi-restraints excluded: chain E residue 953 VAL Chi-restraints excluded: chain E residue 996 VAL Chi-restraints excluded: chain E residue 1004 SER Chi-restraints excluded: chain E residue 1026 VAL Chi-restraints excluded: chain F residue 248 CYS Chi-restraints excluded: chain F residue 363 VAL Chi-restraints excluded: chain F residue 399 ASP Chi-restraints excluded: chain F residue 435 THR Chi-restraints excluded: chain F residue 443 ASN Chi-restraints excluded: chain F residue 524 VAL Chi-restraints excluded: chain F residue 528 LEU Chi-restraints excluded: chain F residue 628 VAL Chi-restraints excluded: chain F residue 640 LYS Chi-restraints excluded: chain F residue 664 VAL Chi-restraints excluded: chain F residue 752 ASP Chi-restraints excluded: chain F residue 959 ASP Chi-restraints excluded: chain F residue 968 GLN Chi-restraints excluded: chain F residue 996 VAL Chi-restraints excluded: chain F residue 1004 SER Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 179 ARG Chi-restraints excluded: chain D residue 273 THR Chi-restraints excluded: chain D residue 276 SER Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 344 GLN Chi-restraints excluded: chain D residue 382 CYS Chi-restraints excluded: chain D residue 470 ILE Chi-restraints excluded: chain D residue 481 VAL Chi-restraints excluded: chain D residue 524 VAL Chi-restraints excluded: chain D residue 567 CYS Chi-restraints excluded: chain D residue 645 ILE Chi-restraints excluded: chain D residue 736 HIS Chi-restraints excluded: chain D residue 742 THR Chi-restraints excluded: chain D residue 749 ASP Chi-restraints excluded: chain D residue 755 VAL Chi-restraints excluded: chain D residue 960 LEU Chi-restraints excluded: chain D residue 996 VAL Chi-restraints excluded: chain C residue 1 VAL Chi-restraints excluded: chain C residue 16 LYS Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 113 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 172 optimal weight: 2.9990 chunk 238 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 75 optimal weight: 0.0870 chunk 68 optimal weight: 5.9990 chunk 191 optimal weight: 1.9990 chunk 187 optimal weight: 2.9990 chunk 79 optimal weight: 0.6980 chunk 53 optimal weight: 5.9990 chunk 40 optimal weight: 0.1980 chunk 223 optimal weight: 2.9990 overall best weight: 1.1962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 569 HIS E 723 ASN ** F 797 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 475 HIS G 2 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.179068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.135687 restraints weight = 28972.870| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 2.13 r_work: 0.3324 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3190 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3221 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3221 r_free = 0.3221 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.56 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3221 r_free = 0.3221 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.57 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3221 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.2833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.160 23579 Z= 0.192 Angle : 0.549 8.615 32062 Z= 0.287 Chirality : 0.044 0.210 3407 Planarity : 0.004 0.049 4125 Dihedral : 5.259 80.874 3475 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.74 % Favored : 95.19 % Rotamer: Outliers : 2.84 % Allowed : 15.33 % Favored : 81.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.15), residues: 2934 helix: 1.91 (0.23), residues: 536 sheet: -1.31 (0.26), residues: 354 loop : -0.88 (0.13), residues: 2044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP F 796 HIS 0.007 0.001 HIS E 550 PHE 0.015 0.001 PHE 2 280 TYR 0.026 0.002 TYR 2 183 ARG 0.008 0.000 ARG E 392 Details of bonding type rmsd link_NAG-ASN : bond 0.00211 ( 13) link_NAG-ASN : angle 1.67016 ( 39) link_BETA1-4 : bond 0.00320 ( 3) link_BETA1-4 : angle 1.50973 ( 9) hydrogen bonds : bond 0.03263 ( 765) hydrogen bonds : angle 4.72104 ( 2352) SS BOND : bond 0.00365 ( 93) SS BOND : angle 1.09666 ( 186) covalent geometry : bond 0.00466 (23468) covalent geometry : angle 0.54078 (31828) Misc. bond : bond 0.11944 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5868 Ramachandran restraints generated. 2934 Oldfield, 0 Emsley, 2934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5868 Ramachandran restraints generated. 2934 Oldfield, 0 Emsley, 2934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 2433 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 229 time to evaluate : 2.803 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 202 ARG cc_start: 0.8478 (mtm-85) cc_final: 0.7881 (mmm160) REVERT: 2 308 ASP cc_start: 0.8766 (t0) cc_final: 0.8498 (t0) REVERT: E 299 ASP cc_start: 0.6176 (m-30) cc_final: 0.5748 (m-30) REVERT: E 406 GLU cc_start: 0.7398 (mp0) cc_final: 0.6858 (mp0) REVERT: E 466 GLU cc_start: 0.6573 (OUTLIER) cc_final: 0.6242 (pm20) REVERT: E 532 HIS cc_start: 0.8617 (t-90) cc_final: 0.8350 (t70) REVERT: E 544 GLU cc_start: 0.7792 (tm-30) cc_final: 0.7063 (tt0) REVERT: E 671 LEU cc_start: 0.8656 (OUTLIER) cc_final: 0.8351 (mm) REVERT: E 745 ASP cc_start: 0.8858 (p0) cc_final: 0.8574 (p0) REVERT: E 764 GLU cc_start: 0.8350 (mm-30) cc_final: 0.7923 (pt0) REVERT: E 820 GLU cc_start: 0.8561 (mm-30) cc_final: 0.8281 (mt-10) REVERT: E 855 MET cc_start: 0.7139 (ttm) cc_final: 0.6882 (ttm) REVERT: E 995 GLU cc_start: 0.7659 (tt0) cc_final: 0.7450 (tm-30) REVERT: F 167 MET cc_start: 0.6439 (mmp) cc_final: 0.5943 (ttp) REVERT: F 187 ASN cc_start: 0.8640 (t0) cc_final: 0.7801 (t0) REVERT: F 240 HIS cc_start: 0.6683 (p90) cc_final: 0.6033 (p90) REVERT: F 360 ASP cc_start: 0.8426 (m-30) cc_final: 0.8214 (m-30) REVERT: F 645 ILE cc_start: 0.7884 (mm) cc_final: 0.7515 (pt) REVERT: F 801 HIS cc_start: 0.7202 (m-70) cc_final: 0.6966 (m90) REVERT: F 903 TRP cc_start: 0.8199 (m-10) cc_final: 0.7904 (m100) REVERT: F 922 TRP cc_start: 0.8158 (m100) cc_final: 0.7888 (m100) REVERT: F 938 CYS cc_start: 0.6954 (m) cc_final: 0.6666 (m) REVERT: D 344 GLN cc_start: 0.8407 (OUTLIER) cc_final: 0.6984 (mp10) REVERT: D 550 HIS cc_start: 0.8230 (p-80) cc_final: 0.7902 (p90) REVERT: D 580 TYR cc_start: 0.8578 (p90) cc_final: 0.8047 (p90) REVERT: D 618 HIS cc_start: 0.7348 (m-70) cc_final: 0.6717 (m170) REVERT: D 736 HIS cc_start: 0.4769 (OUTLIER) cc_final: 0.4237 (p-80) REVERT: D 742 THR cc_start: 0.7903 (OUTLIER) cc_final: 0.7563 (m) REVERT: D 825 ARG cc_start: 0.8643 (ptt180) cc_final: 0.8044 (ptt-90) REVERT: D 922 TRP cc_start: 0.8463 (m100) cc_final: 0.8022 (m100) REVERT: D 1004 SER cc_start: 0.8765 (t) cc_final: 0.7987 (p) REVERT: C 56 LYS cc_start: 0.8056 (tttt) cc_final: 0.7565 (mmtt) REVERT: C 126 ASP cc_start: 0.8955 (t70) cc_final: 0.8711 (t0) REVERT: G 14 LEU cc_start: 0.8668 (tp) cc_final: 0.8279 (tp) outliers start: 69 outliers final: 56 residues processed: 279 average time/residue: 0.4191 time to fit residues: 190.1941 Evaluate side-chains 282 residues out of total 2433 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 221 time to evaluate : 2.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 89 VAL Chi-restraints excluded: chain 2 residue 95 ASN Chi-restraints excluded: chain 2 residue 163 THR Chi-restraints excluded: chain 2 residue 171 LEU Chi-restraints excluded: chain 2 residue 178 VAL Chi-restraints excluded: chain 2 residue 184 SER Chi-restraints excluded: chain E residue 266 LEU Chi-restraints excluded: chain E residue 350 TRP Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain E residue 426 VAL Chi-restraints excluded: chain E residue 448 SER Chi-restraints excluded: chain E residue 466 GLU Chi-restraints excluded: chain E residue 481 VAL Chi-restraints excluded: chain E residue 485 ILE Chi-restraints excluded: chain E residue 523 THR Chi-restraints excluded: chain E residue 671 LEU Chi-restraints excluded: chain E residue 690 LEU Chi-restraints excluded: chain E residue 938 CYS Chi-restraints excluded: chain E residue 949 SER Chi-restraints excluded: chain E residue 953 VAL Chi-restraints excluded: chain E residue 962 ASP Chi-restraints excluded: chain E residue 996 VAL Chi-restraints excluded: chain E residue 1004 SER Chi-restraints excluded: chain E residue 1026 VAL Chi-restraints excluded: chain F residue 248 CYS Chi-restraints excluded: chain F residue 363 VAL Chi-restraints excluded: chain F residue 367 ASP Chi-restraints excluded: chain F residue 399 ASP Chi-restraints excluded: chain F residue 435 THR Chi-restraints excluded: chain F residue 443 ASN Chi-restraints excluded: chain F residue 524 VAL Chi-restraints excluded: chain F residue 528 LEU Chi-restraints excluded: chain F residue 628 VAL Chi-restraints excluded: chain F residue 640 LYS Chi-restraints excluded: chain F residue 664 VAL Chi-restraints excluded: chain F residue 752 ASP Chi-restraints excluded: chain F residue 914 LEU Chi-restraints excluded: chain F residue 959 ASP Chi-restraints excluded: chain F residue 996 VAL Chi-restraints excluded: chain F residue 1004 SER Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 179 ARG Chi-restraints excluded: chain D residue 273 THR Chi-restraints excluded: chain D residue 276 SER Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 344 GLN Chi-restraints excluded: chain D residue 382 CYS Chi-restraints excluded: chain D residue 470 ILE Chi-restraints excluded: chain D residue 481 VAL Chi-restraints excluded: chain D residue 524 VAL Chi-restraints excluded: chain D residue 567 CYS Chi-restraints excluded: chain D residue 645 ILE Chi-restraints excluded: chain D residue 736 HIS Chi-restraints excluded: chain D residue 742 THR Chi-restraints excluded: chain D residue 749 ASP Chi-restraints excluded: chain D residue 755 VAL Chi-restraints excluded: chain D residue 996 VAL Chi-restraints excluded: chain C residue 1 VAL Chi-restraints excluded: chain C residue 16 LYS Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 113 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 225 optimal weight: 0.8980 chunk 62 optimal weight: 4.9990 chunk 153 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 171 optimal weight: 0.0270 chunk 223 optimal weight: 2.9990 chunk 285 optimal weight: 1.9990 chunk 150 optimal weight: 0.9990 chunk 183 optimal weight: 2.9990 chunk 189 optimal weight: 2.9990 chunk 119 optimal weight: 6.9990 overall best weight: 1.1844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 723 ASN ** F 797 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 968 GLN D 475 HIS G 2 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.176981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.139509 restraints weight = 28968.314| |-----------------------------------------------------------------------------| r_work (start): 0.3649 rms_B_bonded: 2.17 r_work: 0.3317 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3170 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3185 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3185 r_free = 0.3185 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.57 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3185 r_free = 0.3185 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.61 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3185 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.2942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.156 23579 Z= 0.190 Angle : 0.551 9.624 32062 Z= 0.287 Chirality : 0.044 0.212 3407 Planarity : 0.004 0.049 4125 Dihedral : 5.275 81.287 3475 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.81 % Favored : 95.13 % Rotamer: Outliers : 2.84 % Allowed : 15.17 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.15), residues: 2934 helix: 1.91 (0.22), residues: 536 sheet: -1.34 (0.25), residues: 363 loop : -0.88 (0.13), residues: 2035 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP F 796 HIS 0.007 0.001 HIS E 550 PHE 0.014 0.001 PHE 2 280 TYR 0.024 0.002 TYR 2 183 ARG 0.008 0.000 ARG E 392 Details of bonding type rmsd link_NAG-ASN : bond 0.00211 ( 13) link_NAG-ASN : angle 1.70266 ( 39) link_BETA1-4 : bond 0.00375 ( 3) link_BETA1-4 : angle 1.51623 ( 9) hydrogen bonds : bond 0.03230 ( 765) hydrogen bonds : angle 4.74430 ( 2352) SS BOND : bond 0.00357 ( 93) SS BOND : angle 1.09524 ( 186) covalent geometry : bond 0.00462 (23468) covalent geometry : angle 0.54284 (31828) Misc. bond : bond 0.11746 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5868 Ramachandran restraints generated. 2934 Oldfield, 0 Emsley, 2934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5868 Ramachandran restraints generated. 2934 Oldfield, 0 Emsley, 2934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 2433 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 227 time to evaluate : 2.457 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 202 ARG cc_start: 0.8531 (mtm-85) cc_final: 0.7916 (mmm160) REVERT: 2 308 ASP cc_start: 0.8842 (t0) cc_final: 0.8581 (t0) REVERT: E 299 ASP cc_start: 0.6207 (m-30) cc_final: 0.5782 (m-30) REVERT: E 359 GLU cc_start: 0.5996 (tt0) cc_final: 0.5793 (tt0) REVERT: E 406 GLU cc_start: 0.7440 (mp0) cc_final: 0.6912 (mp0) REVERT: E 439 LEU cc_start: 0.9037 (mt) cc_final: 0.8707 (mp) REVERT: E 463 ASP cc_start: 0.5333 (p0) cc_final: 0.4866 (t0) REVERT: E 466 GLU cc_start: 0.6773 (OUTLIER) cc_final: 0.6462 (pm20) REVERT: E 532 HIS cc_start: 0.8650 (t-90) cc_final: 0.8410 (t70) REVERT: E 544 GLU cc_start: 0.7769 (tm-30) cc_final: 0.6950 (tt0) REVERT: E 671 LEU cc_start: 0.8681 (OUTLIER) cc_final: 0.8370 (mm) REVERT: E 745 ASP cc_start: 0.8955 (p0) cc_final: 0.8687 (p0) REVERT: E 764 GLU cc_start: 0.8320 (mm-30) cc_final: 0.7843 (pt0) REVERT: E 820 GLU cc_start: 0.8609 (mm-30) cc_final: 0.8387 (mt-10) REVERT: E 995 GLU cc_start: 0.7745 (tt0) cc_final: 0.7489 (tm-30) REVERT: F 167 MET cc_start: 0.6555 (mmp) cc_final: 0.6019 (ttp) REVERT: F 187 ASN cc_start: 0.8671 (t0) cc_final: 0.7870 (t0) REVERT: F 240 HIS cc_start: 0.6737 (p90) cc_final: 0.6100 (p90) REVERT: F 801 HIS cc_start: 0.7266 (m-70) cc_final: 0.7020 (m90) REVERT: F 903 TRP cc_start: 0.8229 (m-10) cc_final: 0.8021 (m100) REVERT: F 922 TRP cc_start: 0.8206 (m100) cc_final: 0.7932 (m100) REVERT: F 938 CYS cc_start: 0.7060 (m) cc_final: 0.6786 (m) REVERT: D 344 GLN cc_start: 0.8395 (OUTLIER) cc_final: 0.6955 (mp10) REVERT: D 550 HIS cc_start: 0.8280 (p-80) cc_final: 0.7949 (p90) REVERT: D 580 TYR cc_start: 0.8630 (p90) cc_final: 0.8000 (p90) REVERT: D 618 HIS cc_start: 0.7370 (m-70) cc_final: 0.6757 (m170) REVERT: D 736 HIS cc_start: 0.4798 (OUTLIER) cc_final: 0.4258 (p-80) REVERT: D 742 THR cc_start: 0.8057 (OUTLIER) cc_final: 0.7747 (m) REVERT: D 825 ARG cc_start: 0.8696 (ptt180) cc_final: 0.8099 (ptt-90) REVERT: D 922 TRP cc_start: 0.8425 (m100) cc_final: 0.8114 (m100) REVERT: D 1004 SER cc_start: 0.8792 (t) cc_final: 0.8026 (p) REVERT: C 56 LYS cc_start: 0.8137 (tttt) cc_final: 0.7593 (mmtt) REVERT: C 126 ASP cc_start: 0.9011 (t70) cc_final: 0.8776 (t0) outliers start: 69 outliers final: 58 residues processed: 275 average time/residue: 0.3462 time to fit residues: 153.2317 Evaluate side-chains 283 residues out of total 2433 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 220 time to evaluate : 2.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 89 VAL Chi-restraints excluded: chain 2 residue 95 ASN Chi-restraints excluded: chain 2 residue 163 THR Chi-restraints excluded: chain 2 residue 171 LEU Chi-restraints excluded: chain 2 residue 178 VAL Chi-restraints excluded: chain 2 residue 184 SER Chi-restraints excluded: chain E residue 266 LEU Chi-restraints excluded: chain E residue 350 TRP Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain E residue 426 VAL Chi-restraints excluded: chain E residue 430 ILE Chi-restraints excluded: chain E residue 448 SER Chi-restraints excluded: chain E residue 466 GLU Chi-restraints excluded: chain E residue 481 VAL Chi-restraints excluded: chain E residue 485 ILE Chi-restraints excluded: chain E residue 523 THR Chi-restraints excluded: chain E residue 671 LEU Chi-restraints excluded: chain E residue 690 LEU Chi-restraints excluded: chain E residue 938 CYS Chi-restraints excluded: chain E residue 949 SER Chi-restraints excluded: chain E residue 953 VAL Chi-restraints excluded: chain E residue 962 ASP Chi-restraints excluded: chain E residue 996 VAL Chi-restraints excluded: chain E residue 1004 SER Chi-restraints excluded: chain E residue 1026 VAL Chi-restraints excluded: chain F residue 248 CYS Chi-restraints excluded: chain F residue 363 VAL Chi-restraints excluded: chain F residue 367 ASP Chi-restraints excluded: chain F residue 399 ASP Chi-restraints excluded: chain F residue 435 THR Chi-restraints excluded: chain F residue 524 VAL Chi-restraints excluded: chain F residue 528 LEU Chi-restraints excluded: chain F residue 628 VAL Chi-restraints excluded: chain F residue 640 LYS Chi-restraints excluded: chain F residue 655 THR Chi-restraints excluded: chain F residue 664 VAL Chi-restraints excluded: chain F residue 752 ASP Chi-restraints excluded: chain F residue 914 LEU Chi-restraints excluded: chain F residue 959 ASP Chi-restraints excluded: chain F residue 996 VAL Chi-restraints excluded: chain F residue 1004 SER Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 179 ARG Chi-restraints excluded: chain D residue 273 THR Chi-restraints excluded: chain D residue 276 SER Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 344 GLN Chi-restraints excluded: chain D residue 382 CYS Chi-restraints excluded: chain D residue 470 ILE Chi-restraints excluded: chain D residue 481 VAL Chi-restraints excluded: chain D residue 524 VAL Chi-restraints excluded: chain D residue 567 CYS Chi-restraints excluded: chain D residue 645 ILE Chi-restraints excluded: chain D residue 736 HIS Chi-restraints excluded: chain D residue 742 THR Chi-restraints excluded: chain D residue 749 ASP Chi-restraints excluded: chain D residue 755 VAL Chi-restraints excluded: chain D residue 960 LEU Chi-restraints excluded: chain D residue 996 VAL Chi-restraints excluded: chain C residue 1 VAL Chi-restraints excluded: chain C residue 16 LYS Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 113 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 87 optimal weight: 1.9990 chunk 212 optimal weight: 0.5980 chunk 27 optimal weight: 0.4980 chunk 283 optimal weight: 3.9990 chunk 30 optimal weight: 4.9990 chunk 5 optimal weight: 0.0980 chunk 58 optimal weight: 0.8980 chunk 142 optimal weight: 0.9990 chunk 57 optimal weight: 3.9990 chunk 255 optimal weight: 0.1980 chunk 47 optimal weight: 0.8980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 723 ASN ** F 797 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 968 GLN D 327 HIS D 475 HIS ** D 736 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 994 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 2 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.180364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.141510 restraints weight = 28755.505| |-----------------------------------------------------------------------------| r_work (start): 0.3649 rms_B_bonded: 2.06 r_work: 0.3384 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3247 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3256 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3256 r_free = 0.3256 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.61 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3256 r_free = 0.3256 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.52 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3256 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.3002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.093 23579 Z= 0.115 Angle : 0.505 9.225 32062 Z= 0.264 Chirality : 0.042 0.174 3407 Planarity : 0.004 0.047 4125 Dihedral : 5.004 80.739 3475 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.06 % Favored : 95.88 % Rotamer: Outliers : 2.26 % Allowed : 15.87 % Favored : 81.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.15), residues: 2934 helix: 2.21 (0.23), residues: 537 sheet: -1.16 (0.26), residues: 340 loop : -0.82 (0.13), residues: 2057 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP F 796 HIS 0.006 0.001 HIS E 550 PHE 0.012 0.001 PHE G 118 TYR 0.025 0.001 TYR 2 183 ARG 0.008 0.000 ARG E 392 Details of bonding type rmsd link_NAG-ASN : bond 0.00187 ( 13) link_NAG-ASN : angle 1.45212 ( 39) link_BETA1-4 : bond 0.00307 ( 3) link_BETA1-4 : angle 1.21606 ( 9) hydrogen bonds : bond 0.02899 ( 765) hydrogen bonds : angle 4.49612 ( 2352) SS BOND : bond 0.00219 ( 93) SS BOND : angle 0.86538 ( 186) covalent geometry : bond 0.00280 (23468) covalent geometry : angle 0.49910 (31828) Misc. bond : bond 0.07822 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15732.76 seconds wall clock time: 273 minutes 42.97 seconds (16422.97 seconds total)